Just to double check, you have restarted the IDE after making this change to VA's stable directories list, and let VA rebuild its symbol databases?
Can you try putting the test project into a dummy directory on C:, to remove the subst drive letter completely from the equation?
I should have been testing the same situation as you, but so far I have not been able to reproduce these problems. I am wondering if there is some additional factor we are missing.
Probably, but I've now got a shiny new desktop where everything seems to be working. (Though this machine has a second physical disk, so I'm no longer substing anything)