Quick update:
I haven't had any signs of these issues recently, although I haven't been running the external script to update referenced .dlls. So, it appears that the ncrunch update has resolved the other issues I was seeing.
I did notice an instance a few minutes ago where NCrunch said it was not able to build my test project due to undefined classes, which were actually defined in another project. However, within 60 seconds, the issue resolved itself and the builds completed. During this time, I made no changes to files, and aside from clicking the links in the NCrunch test output window, the only action I took was to close a single open file. So if the issues does still exist, it's at least very short lived.
Good work!
thanks
~john