Can't use the shift/control button to toggle (shift = remove quantity), (control = remove stack) when you have the supply depot open AND you've searched for something. Removing the filter restores the functionality.
Had this happen to me last week. If you try to search for an item manually, it disables the ability to remove said item in any quantity besides one at a time.
You have to use partial words. Like roo for root. Or ele for electrum, iro for iron, etc. Big pain. Too bad we can't search for mats by quest.
Oddly, if you search for something and it's second, third, or later on the list, you can use ctrl/shift to grab more than one at a time. It's only the first search result that's bugged. I think maybe the first item in a non-filtered list is also bugged?