All works now, checked repeated closing and launching.
I had to search for the protocol.mat files, now I know there is one for each experimental Protocol. They only seem to update if I switch to a particular Protocol, then exit BSt. All 4 of mine have been regenerated at this point.
The odd thing, though, is that when I launch Matlab, I still get this warning:
Warning: Name is nonexistent or not a directory: D:\Research\Matlab projects\iso2mesh-1.9.6-allinone\iso2mesh-1.9.6
So that is a Matlab problem, not a BSt problem. Matlab still seems to have this stored somewhere. I wonder what process of Matlab start-up needs to be reset to make this go away. I am not facile with this sort of Matlab manipulation.
Thanks for your help so far. I will try the iso2mesh now.