The only one I've had a problem with is the spools of thread. I found with the bolts of cloth that if I tried to start a new one too fast, the one I'd just made didn't stack, but when I slowed down my macro click (last object/last target, before anyone asks AND it works from a secure!) it sorted that out.
My workaround for the spools of thread at the moment is to use the UOA organiser agent. They stack when dropped in the bag/pouch/pack and can be used on a loom from there, so you don't even have to take them out again