I recently found out that the emulator power up/down wasn't working properly with AT&T UnixPC 3B1/7300. The issue and solution is documented at.
http://www.pdp8online.com/mfm/ttl_driver.shtml. This will be seen with controllers that uses TTL totem pole drivers instead of open collector. The OMTI 5200 also has this issue.
I also found a bug where if you had a seek error on reading a disk the emulator file created was bad. Fixed in current code along with various minor bugs rearranged and new formats added.