https://bugs.winehq.org/show_bug.cgi?id=41625
--- Comment #11 from Austin English austinenglish@gmail.com --- (In reply to sg7jimr from comment #10)
A number of users have been discussing this issue in the Star Trek Online forums. From trial and error it seems Wine 1.6.2 is not affected by this problem, and running the game on Wine 1.6.2 can lead to the game working again in later versions. The problem appears to be related to pixel shader compilation, the compile is failing on recent Wine versions but 1.6.2 succeeds and then anything it has compiled is OK in any version.
Could you / someone git bisect between 1.6.2 and 1.9.x? http://wiki.winehq.org/RegressionTesting