I am unable to find any true fixes for this so far, aside from disabling SLI mode in the nvidia control panel. Basically, when it rains, water ripples double up on themselves and do not behave properly when SLI mode is enabled. Is there a way to correct this, without disabling SLI in the game's profile?

After enabling SLI, did you make sure Oblivion regenerated your INI and hardware profile files (in the same folder as the Oblivion.ini.) One is called renderinfo.txt and I forget the name of the other. See if that helps.