Here is an updated version of the patches. Can you retest the games? (the ones that worked already as well as the broken ones)
What are the differences?
-> Proper handling of RHW vertices which do not come from a vbo(should fix Star Wars Jedi Knight 1) -> Proper handling of the alpha value in the lighting code(+ a test). Fixes the water in AoM.
Those issues had a quite big effect potentially, so more games may be fixed now.