While using Dual Hotbars if Inventory Tweaks tries to refill a used item from the second hotbar we get an IndexOutOfBoundsException.
Crash Log with 1.59-dev-152
Crash Log with 1.59-dev-156

Dual Hotbars dev, RebelKeith, has apparently tried to contact you about this issue.

I can't fix mods doing stupid things that break the way the inventory is laid out.

It doesn't change anything about the way inventory is laid out. The extra hotbar is simply the first row of the inventory.

The refill code is very particular about how it handles the hotbar, it must be at the end of the (player) inventory starting from where the vanilla one is. Trying to put them in different places will confuse the hell out of it.