The Black Screen of Death with the Giant Yellow Cursors is apparently a problem that some people have with Star Trek: Bridge Commander even on Windows Systems.
I had this problem after 9.0.
I finally solved it this way:
Go to 'programs' and 'run command'. Choose your Star Trek Bridge Commander bottle and under 'command' type [regedit] (with no brackets).
hkey_current_user/software/wine
Here, right click on the 'wine' folder and create a 'key' called 'Direct3D'.
In hkey_current_user/software/wine/Direct3D create a 'string' called OffscreenRenderingMode. Right click on the new string and select 'modify'. Under the value, enter [backbuffer] (with no brackets).
Exit from the regedit.
On my machine at least, STBC now works.