I updated the Bootstrap version in Flat Bootstrap v1.6. However, I ended up adding so much to v1.6 that it needs more testing so hasn’t been released yet. Specifically it has Bootstrap v3.3.2 in it.
If you want to help test Flat Bootstrap v1.6, let me know. I could push the latest build of it to my github account for how to download from there. Its pretty stable. I’ve been running it on my production website for a while now.
Also, as a side note, if you are a Bootstrap guru… you could take my specific Bootstrap config file and use that to download the latest version of Bootstrap. Of course it wouldn’t be tested with the theme, but in general they are mostly fixing bugs within the 3.x builds. Be sure not to just grab the “stock” Bootstrap, though, because I’ve made a LOT of changes to it so that I don’t have to have even more CSS overrides within the theme.