Allangrant, as you stated you are a back end developer. While that's good to note, it doesn't exclude the outcome that DHH and the community have already commented on.
However, I think something that is missing is a little more guidance. Other than the issues others have communicated, the web page showed that your company hasn't established, even in very raw form, it's own style that is best for its users. It's normal to reflect and be inspired by others designs. I would even recommend that you take screenshots of the design styles that speak to you. From that point though, the screen shots should be used as "internal" discussion materials that help your company find the essence of its own style. That style should always be taking what's best for your product/service and user base, into the style characteristics.
Once you've found your core style, express it and iterate over it using each iteration as a piece of more relavent inspiration to your style (37Signals recently released a cool video on their blog that demonstrates this process through their eyes). The results should make you proud enough to express and share it with your customers. Only at that point do you finally make it public. After that keep iterating over it. If you utilize external inspiration, make sure that you've iterated over it enough that your style doesn't feel like a knockoff. You should be able to identify this easily and odds are, if you've been going through all this it won't be. However, if you have concerns just take screen shots of your style and the screen shots of what externally inspired you,...show them to some people who don't work for your company and weren't involved with the design process. They should be able to 1) pick up on your style and 2) agree that it isn't a knockoff. Given the situation you are in, I would recommend this heavily to help give piece of mind.
I realize that you wanted to gain from the lessons learned from 37Signals internal design iteration process as well as other companies. However, if you note what I said above, it means they were focusing "also" on their product and their customers. Which means if you directly reflect your design from theirs, you weren't focusing enough on your customers. You might have intended to give your customers a great design experience, but without going through the process above, your website is considered not authentic...and as a result people focus on the their feeling of "this looks oddly familiar" instead of focusing on what your product can do for them.
Many, if not all of the people who have commented have gone through their own artistic design process to build one or more designs. And at times it can be "hell" (fun, but still) to create something that the designer feels is good enough to share/use. It is a compliment that someone is inspired by your design. But when it's closer to a knockoff it can make the designer feel like they sacrificed him/her-self for your free ride. If they intended for it to be given away, then the benefit you receive gives them whatever good feeling they were looking for. I'm sure you have, like many people, worked insane hours that took away from family, friends, and even yourself.
I hope humility, honesty, and hard work guide your company to a design that you can be proud of.
I do have to say, based on the evidence that DHH keeps unearthing, it does not seem like your company has put forth the immediate effort needed to represent that your company is taking to heart what is being said by DHH and others. That unfortunately is effectively like a strike 2. First for the action, and secondly for the inaction. Yes the inaction is both in relation to PR and actual outcome of change.
For the future viability of your company, you might consider immediately removing all content and styles even remotely considered to be "borrowed" (by any definition)...even if it means your websites are bland and almost blank. That however only closes the door on any indiscretions. Going through the challenges of repentance and acquiring forgiveness, is something only your company's heart can achieve. Seeking guidance would also probably be a good idea to get you through this current PR issue.
On your twitter pic it shows that you wish to stop sopa. In a recent case, GoDaddy had their own PR problem that cost them dearly. Given that your company is a start up, even with $1.2M in funding, appropriately negative PR like this can cost the company it's life.
*PS: 37Signals has 2 good books to read. I believe "Rework" even has some comments regarding when you screw up as a company. However, since it is the authors themselves to which your company has afflicted....
I hope your company is able to make the right choices.
However, I think something that is missing is a little more guidance. Other than the issues others have communicated, the web page showed that your company hasn't established, even in very raw form, it's own style that is best for its users. It's normal to reflect and be inspired by others designs. I would even recommend that you take screenshots of the design styles that speak to you. From that point though, the screen shots should be used as "internal" discussion materials that help your company find the essence of its own style. That style should always be taking what's best for your product/service and user base, into the style characteristics.
Once you've found your core style, express it and iterate over it using each iteration as a piece of more relavent inspiration to your style (37Signals recently released a cool video on their blog that demonstrates this process through their eyes). The results should make you proud enough to express and share it with your customers. Only at that point do you finally make it public. After that keep iterating over it. If you utilize external inspiration, make sure that you've iterated over it enough that your style doesn't feel like a knockoff. You should be able to identify this easily and odds are, if you've been going through all this it won't be. However, if you have concerns just take screen shots of your style and the screen shots of what externally inspired you,...show them to some people who don't work for your company and weren't involved with the design process. They should be able to 1) pick up on your style and 2) agree that it isn't a knockoff. Given the situation you are in, I would recommend this heavily to help give piece of mind.
I realize that you wanted to gain from the lessons learned from 37Signals internal design iteration process as well as other companies. However, if you note what I said above, it means they were focusing "also" on their product and their customers. Which means if you directly reflect your design from theirs, you weren't focusing enough on your customers. You might have intended to give your customers a great design experience, but without going through the process above, your website is considered not authentic...and as a result people focus on the their feeling of "this looks oddly familiar" instead of focusing on what your product can do for them.
Many, if not all of the people who have commented have gone through their own artistic design process to build one or more designs. And at times it can be "hell" (fun, but still) to create something that the designer feels is good enough to share/use. It is a compliment that someone is inspired by your design. But when it's closer to a knockoff it can make the designer feel like they sacrificed him/her-self for your free ride. If they intended for it to be given away, then the benefit you receive gives them whatever good feeling they were looking for. I'm sure you have, like many people, worked insane hours that took away from family, friends, and even yourself.
I hope humility, honesty, and hard work guide your company to a design that you can be proud of.
Good luck and I hope this all helps.