Alright, so after some testing I figured out the problem.
If you don't select the algorithm FIRST in Endmember Collection, apparently only the stats necessary to compute with the selected algorithm are imported. So, if you import the spectra with the default selection (parallelpiped) then switch to MLC or something which requires the covariance information, then you'll get the problem I was having. You must select the algorithm first, and then import the spectra, then there's no problem.
It's an easy enough workaround, and maybe this would be obvious to someone else, but it wasn't to me and it created a rather perplexing error situation. It seems that it would be an easy fix to either import all the stats regardless of the selected algorithm, or to re-import the necessary info when the algorithm is switched. My argument here is that it's an interactive tool, and the order of operations here should be inconsequential. I don't know if it qualifies as a "bug" but it's certainly an easily fixed nuisance.
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