I have tested this with Age of Myhology (Titans 1.03) on wine-1.1.7-106-g38815e1, patches 1-11 don't seem to cause any problems (haven't checked extensively though), but upon applying the 12th (0012-WineD3D-ARBvp-ffp-replacement.patch) the water lost it's transparency [1].
Sounds as if there's a problem with texture coordinates. Can you file a bugreport and assign it to me? Please add a link to a downloadable demo if one exists