Battle of Olympus is a great example. If I have time maybe I can get some shots of Faxanadu as well, but I think these pictures to a great job explaining the problem.
Honestly, I'll have to look harder for the manual.doc. I thought the only documentation for this emulator was the 4 videos and I don't have the attention span to watch videos without somebody explaining what's going on. A manual will be a huge help. I'll be sure to check it out before I do anymore work.
EDITED TO ADD: I did manage to get the delete button to fix a few similar things in Blaster Master, but I was unable to get it to fix the above problem in Battle of Olympus.