What sort of foot are you using?
With or without a walking foot my Janome does shorter-than-normal-sewing stitches in rev. And I don't think walking feet are designed to reverse anyway are they, based on the teeth gripping fabric and moving it towards the back with each needle rise/fall? The mechanism in the WF doesn't recognise that the machine is in rev. If you are using a jumping foot with feed dogs down it wouldn't matter 'cos you wouldn't need to be in reverse.
I guess I could try pulling more to bring the stitches to the "normal" size but with my luck I would break something - a needle, a sewing foot, my neck as I fell backwards out of my chair, . . . . .
I would quilt all the short sides (two per HST) in a zig-zag top-to-bottom of the quilt, then go back and do all the hypoteneuse (hypoteneuses, hyptoenii, sp?) top-to-bottom of the quilt. Lots of thread ends, but easier sewing and the degree of extra work would depend on how you finish your thread ends.
Good luck with the project.