Hi Graham,
this sounds like hardware issue. I can't easily imagine any common software or DAW issue, which can cause the problem. On the other hand, some failing cap at one channel (and associated temporary decrease of output level) will be more probable cause, according to gradual nature of that.
If you have free pair of physical outs, you can certainly try to connect monitors there and reroute monitor bus at console there. If you find, it's fine, then only main outs are affected. I don't know how often that happens, but if you want to have some proof for that (say for some RMA), then I would connect affected outputs back to inputs using some loopback cable, run some sine generator from DAW and record that back to another track.
I don't know, how old the interface is, but if you'll be sure, it's HW issue, I would try to apply warranty there.
Michal