Inventory-Profiles displays the sorting buttons on GUIs that look like inventories but actually are not. They usually are GUIs of other mods like slotlink, storage cabinet or tcrafting. Trying to use the buttons on those screens does nothing at best, or gives weird results at worst.

Would it possible to have a file/option/whatever that would allow to list GUIs to be ignored by Inventory-Profiles ? (which could come with sensible defaults)

This is also the case with Applied Energystics inventories, which are technically storage inventories, but don't work the same way as chests.

This mod attempts to treat the AE2 storage terminal as a chest. When you use an ME Crafting terminal (I haven't tested with other terminal types), middle clicking attempts to sort the inventory, but causes unexpected behaviour.

If you have any locked slots (locked using Inventory profiles) it will send them into the crafting grid for the terminal instead of leaving them where they are. Ae2 treats this grid as part of the network storage, and not player inventory, so those items get absorbed into the network when you leave the terminal or start crafting anything else.

It also seems to take random items out of the storage network, although I can't reliably repeat this.

Finally, the default sort hotkey (r) still gets triggered while typing in AE2's search bar, causing you to accidentally sort your inventory. This is easily fixed by changing the sort hotkey to middle mouse however.