[work not getting done in some shops]
Workshop profiles could cause that. If you, for instance, set the "maximum skill level" below legendary and assign it to a dwarf, the dwarf will stop using the workshop once he reaches legendary skill. Similar problems occur when setting the minimum skill level then assigning an odd job that no one has the necessary skill for (e.g. metal cabinet).
Of course it could be something entirely different as well. It is rather difficult to accurately diagnose problems based on assumptions of the likely state of your game; if you want a direct answer the best bet is to post a save on DFFD so that someone can investigate the problem.
Definitely not profiles, in at least one case, it was a legendary dwarf assigned to a legendary-only workshop (which she had gladly used earlier before the issue occurred). And I tried fiddling with the lower bound permissions just in-case, to no effect.
Did you remove the lower bound entirely? I've only witnessed it in older versions, but there was never a fix report:
Dwarfs with "rusty" skills are considered as "dabbling" (= level zero) for the purpose of shop profiles, regardless of their actual skill rating. Furthermore, "rusty" will never display for high-level workers (generally for legendaries, but often at a few levels below as well) even when it applies.
If i want to reserve shops for my high-skilled workers, i generally use a personal, never a skill permission.