Something I've noticed, which is probably not your issue, but could be affecting it slightly is I can't don my Fortify Alchemy gear from the Satchel. I keep my Fortify Alchemy gear (4 pieces at 25% each) in the Apothecary's Satchel on the table in Breezehome. I have to to take the gear out, exit the Satchel, don the gear, and then activate the Alchemy Table for the gear to work.

Hopefully it's what thinzad is proposing because that would be a relatively easy fix.

Edited for accuracy.