When I start up the foundry all of the buttons have black boxes in the top of them, I know it sounds minor, but it is very annoying
I have that too. I thought it was something to do with a laptop running a low video card but when I used Foundry on my desktop with a high-end NVidia graphics card it does the same thing. I can only assume that one of the graphic files was not correctly installed at time of installation on the tool or it is corrupted in the patch.
I can't reproduce this, and I just re-patched to Tribble from scratch.
Do you have any options turned on in your Nvidia control panel? Are you having any graphics issues elsewhere in the game?
No, no adiditonal options turned on with either of my PC's and the main PC with Quad Core and the nvidia card doesnt have any unusua settings. I've uploaded a screenshot to the following site so you can see what I mean. This was taken from my laptop but I'm seeing this also on my desktop too.