I would agree that it's possibly the WD2793 that's gone in one board, you could of course try swapping the one from the other board and see if you get any response.
Also when you say no reponse do you mean literally nothing ? no drive lights come on and the drive motors don't spin ? Typically these functions are controlled by a seperate latch register which is written to independently of the disk control chip. Typically this would be something like a 74LS373, or a similar latch chip, you should be able to determine this by tracing the drive select / motor on lines from the floppy connector.
The Dragon 32/64 DragonDos controlers use the WD2797, and have used this with 3.5" drives without any problem, also the RM Nimbus uses the very same WD2793, with 3.5" drives and works. I guess 3.5" drives where not out when the datasheet was written. I have found for the most part with correctly designed hardware that 3.5" drives and 5.25" can be used interchangably.
Apparently BGMicro have them :
http://www.bgmicro.com/ICS2793.aspx but might be woth contacting them and checking if it does turn out to be a faulty WD2793.
Cheers.
Phill.