The debugger itself is unfortunately a bit of a black box (unless you work within MS). The difference in behaviour is likely to be related to the structure of the PDB file, which NCrunch needs to reconstruct when it instruments the assembly.
To troubleshoot this issue, I'll need to have a sample solution that can produce it consistently in all environments. Unfortunately, there are too many complex interactions between black boxes to identify the issue any other way. If you manage to find a way to reproduce it, you're most welcome to submit code to me through the NCrunch contact form.