No, Linux issues are not fixed - moreover, they've gotten worse with the latest changes, now not only the sideboard window is screwed like it was before, but also the "quit Forge" and many other dialogs are screwed in the same fashion (I think it's simply due to the fact that these dialogs now use the new FDialog though). Moreover, it's impossible to even see many buttons unless you hover the mouse over them... I can't say the game is completely unplayable, but it's visually screwed and its playability is hampered by non-visible buttons in some windows

Something has to be done with this issue, it's almost a dealbreaker for an upcoming beta release. Wish I could help, but I have no experience with the GUI functionality you're implementing, so I'm probably not the best person for that - the best I can do, I guess, is test for you and tell you if anything changes for the better or for worse...
Some examples of screwed up windows:
Quit Forge - usable, but visually screwed:
Concede - usable, but visually screwed:
Sideboard - fubar, not too usable until some mouse motions are performed over the buttons area:
P.S. I like the idea of the new skinned look very much. Wish it was actually usable and not glitchy under Linux, it looks beautiful otherwise.
- Agetian