FWIW, I have exactly the same problem. I have had it on two different bikes with 3 different sets of disk brakes. I have also inspected my current callipers very carefully looking for leaks so I am 99% sure it isn’t leaking callipers in my case. My current theory is that it is oil from my chain getting on to the disk somehow or contamination from lovely London roads. It is damn annoying. Fit new pads and clean disks – lovely braking. A few days later, mysteriously crap rear brake that provides no retardation at all. It drives me mad.
Just in case chain oil is a common denominator between us “suffers”, I use Purple Extreme chain lube. I might change to something more clingy just to see if it helps.