Total sense. As a reformed guitar player, I can tell you that this is a fairly common issue with guitar amps, and is caused by oxidation on the contacts of the jacks. It is NOT serious, but it is puzzling and annoying (in my experience).
I am familiar with the change in loudness behaviour you describe when the fx loop is jumpered. I think the degree of loudness variation depends on whether the loop is series or parallel.
Maybe bass players can learn something from the guitar world after all..
But more technical heads than mine may well chip in at this point.