I often use a tool in main and a block to build in the offhand, but with the restock feature it puts in the fresh stack in place of the main hand, pushing away the tool into the inventory.
Also, (not sure if thats cause of the server Im on, but) when I turn off restock with a hotkey and change dimensions, it gets turned on again.

Which Minecraft and mod version is this on?

The tweak turning back on is caused by a bug in malilib, which has been fixed in the 1.12 versions and thus should be fixed in the next round of updates from 1.12 to 1.13.2 to 1.14.