Greetings.
I haven't tested this plugin with baseparamcontrol, but I don't think that's the issue here, or not exactly, anyway.
What is the actual damage formula of the skill being used? This plugin automatically replaces a.atk (or user.atk) with a special calculation depending on which hand is being used. I suspect that calculation isn't taking the baseparamcontrol into consideration, because like I said, I haven't exactly tested with it. If your damage calculation is something like (a.atk - b.def) -a.mat it could end up returning a weird value that ends up being zero somehow, and results in only your mat being used.