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I'm having this issue as well. I noticed it first a couple of days ago. And these "removed/hidden" items won't appear when requeuing items because they "don't exist". I've done several Force Rescans of the affected professions (JC and Alchemy only ones that I've noticed), relogging, reloading, restarting doesn't seem to fix it. I did notice searching for the desired item in the normal Professions window *sometimes* made _Crafting see it ... eventually.
Hmm...if you make the TSM window slightly bigger so that the "Additional Item Settings" button doesn't wrap to the next line do you get the same problem?
That works, though I have to do it every time I open the window.