very strange indeed. From the first thoughts, I see the problem in VDT 1.21. From 1.33h version write protection of virtual disk drives is implemented. I count only with virtual disks created by EasyHdd by LMN and not VDT 1.21. But I have a test whether Easy Hdd is installed or not, maybe tests are wrong. But definitelly VDT 1.21 is more sophisticated, although the VDT table must be created manually, (in VDT 1.21 write protection can be set for each disk separatelly, whereas by EasyHdd write protection is set for the row 3-128 master or slave disks.)
Actually, on the second line in nmi menu you can see a status of your IDE devices. If they are in colour (green or red), it means that EasyHdd was detected. If they are in white (Master/Slave), means IDE device was detected and no other software able to work with hdd. This should work even in the latest version 1.35fix.
I recommend trying this: nmi menu 1.31x has not write protection implemented (ie. no work with EasyHdd) while 1.33h has. So try out both. If version 1.31x will be working in situations where 1.33h not, then the problem must be as I descibed.
Other thing is that when I was programming the mb-resi copier, once it happened that on my CF card system sectors were erased and the card become completelly unreadable even on PC. But this happened only once, so possibly, also Residos might be a cause of your problem.
Please, try what I have described and let me know. I am using 1.35fix and easyHdd and have no such problem.
Hope it will help, let me definitelly know about the results of your tests.