@Exvoke - If you try to install two completely different mods (and *don't* try Score Timer or Regen Assist) do you see the same issue? What you are seeing sounds like what I am seeing (you see the team lineups, hear the sounds of the battle, can hit buttons/mouse, but you can't see the ships/water/etc - like you are stuck viewing only the lineups while the battle is going on).
I tested with different sets of mods:
1) BadoBest v1, SMI v2, Tech Tree, Sounds when Minimized
2) Smoke Timer left side, Info Panel (self), and Regen Assist
In both cases I saw the same issue and these were with different sets of mods. Wondering if you have issues regardless of which mods you install.
Once I am not pink I will likely test again, but if we have the same issue and each provide logging - it might help pinpoint the issue quicker.