All of their assets were created in-house by DesginModo's designers..
I would say that is the issue in a nutshell. LayerVault is claiming they are the exclusive rights-holders, yet absolutely nothing in Flat-UI is the same as anything on LayerVault's public site.
The only possible angle remaining would be if LayerVault had a bunch of these elements behind their paywall... something tells me that's not the case.
Edit: Alright, I admit the colour Turquoise is used on both pages. Still, I'm fairly confident turquoise boxes (of differing shapes!) are not copyrightable.
LayerVault is obviously pissed that a design similar to their unique design will be used by amateur Bootstrappers all over the web.
You can't patent Colors / Helvetica Neue / Rounded Corner Squares. It just reeks of tactics similar to patent trolls.
I think a while back there was blog theme used that was similar to Svbtle, but there was no take down notice or such nonsense. It generated a decent discussion and conversations about something that's too close in style.
Look at @layervault on Twitter, they are just getting destroyed right now. Even by designers, their main target audience.
If they went along the lines like 'Hey, this is pretty similar to our design. We think it's cool we inspired you but can you deviate it from us a bit more or re-name the project to like Layervault Bootstrap?' I mean why not - have your name in the same conversation as Twitter Bootstrap!
A total botched and missed opportunity.
They look visually similar. As well as dozens of other pieces/sites.
Allan says Designmodo was not being cooperative in emails on the issue, and I think that's the point where you take it to a blog post with examples of the case you're trying to make, rather than forcing Github to shut down an entire project that goes outside of just the illustrations in question.
Their approach seems less about actually proving their worth by focusing on their product and ignoring outside "competition", and more about trying to shut down those that they feel are a threat to them. Not sure what exactly that says about them or the confidence they have in their own product, but it's a bad attitude to have towards innovation and inspiration.