I wish I had something more concrete for you -- mostly it's just an uneducated guess. When I retook the MSF I was on a CBR 250 that had an issue with first gear. It would rev fine with the clutch in, but had a lot of trouble getting past ~3k RPMs in 1st. Once it was past that it was OK. Your problem sounds sort of similar, but I'm not sure.
The fact that you can rev freely with the clutch pulled in but can't when you let it out is telling us something; I just don't know what!
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