One thing I'm curious about, based on that screenshot of the Lisa "PFG" control panel: is the data rate on the Lisa's drive interface slightly different than on the Mac? It talks about initializing the... whatever, at either "15.7mhz" or "16mhz"; I vaguely recall that that the IWM has clock inputs that are nominally either 7mhz or 8mhz depending on whether it's used in an Apple II or a Mac, but the clock signal actually supplied to it in the hardware was more like 7.85mhz. That's less than 5%, and of course the disk controller is supposed to be able to compensate for some degree of disk speed variation, but if the Lisa clocks its controller at a straight 8 mhz is it possible that the data stream coming from the FloppyEmu is just far enough out spec that the Lisa is having trouble locking onto it?

(Totally saying this out of ignorance; I haven't actually looked into what the Lisa hadware looks like at all beyond knowing it's not directly driven by the 6800, etc. It would seem this problem would affect real disks on the Lisa as well anyway... my thought there was that the PWM signal from the Lisa might spin the drive slightly faster than it does in the Mac to make it even, but then it occurred to me that the Lisa can supposedly work with 800k drives that ignore PWM with an upgrade so... yeah, never mind that idea.)