I have recently realized that the merged files in Wrye Bash are colored green, and I can uncheck them in OBMM so they don't load twice. I've had no problems with this with graphics types of things (Better Wine, TNR races, etc.)
However, I did have problems unchecking in OBMM this mod - Better Gem Prices. It reprices my gems to be nicely priced (pearls are 250 and above, more realistic to me than a stupid 2 gold). Anyway when I uncheck this particular mod in OBMM, even though it's green in WB, the gem prices reset to the Vanilla price. I had to check it again in OBMM in order for it to work again.
Why is this?