Fixed it. Evidently, all you have to do is copy the VCrain textures from the FS9 folder to fix this. Did some googling. Also, somebody made a set of rain VC rain textures that are smaller, and, presumeably, less of a frame rate hit. I found those at AVSIM. Search for "vc rain" in the FSX library. These are the ones I installed.
Odd thing is, after doing this research, I seem to remember doing this already before. In fact, the FSX texture folder did contain a set of vc rain files, but the forum I found the solution from said that MS forgot to include the VC rain texture files, and this is what caused the opaque issue.
I wonder if the REX2 installation replaced the VC rain texture files with "broken" ones...