I work with the software developer doing the recent ROM development work for Cloanto, specifically I was doing some hardware compatibility testing on v45.064. Not sure how publicised this bug causing intermittent floppy operation is, but it's been around a bit over a year and observed by a number of users.
And Cloanto now list v45.064 as the current version, they also state that the floppy interrupt problem is fixed in this version.
Updated 2016-10-05, nice!
I have the ROM 3.X in an A600 (with ACA620) and can't remember any floppy drive problems, so either I'm lucky or A600 systems aren't affected at all.