Hi,
I think Analysis is making some math errors somewhere. I can't speak for protein assignments, but in the case of RNAs whenever I try to assign a resonance (this seems to happen for every cross-peak) analysis warns me that that assignment is unlikely to be at this chemical shift. I checked in both the BMRB and in the NmrRefChemicalShift popup and the assignment is legitimate. Also I've used analysis to make these assignments before in another project and I didn't get any error messages.
Thanks,
Justin