I do not know the cause, but if you have two or more stacks of the tome upgrade (common upgrades are 50% stronger) then common attack speed upgrades no longer have any effect.
Uncommon upgrades still work, and previously added common upgrades will work, but no new common attack speed upgrades have an effect.
I have tested it with normal and triple shot staves, and with 0-4 tome upgrades, and with 2, 3, or 4 tomes this bug is present with either staff.