I've noticed more people saying they have the problem recently, which is good because then it's more likely to be fixed.

I've a theory that R0ing causes it.

Earlier I was doing the Ifrit runs, porting to Grid to turn the quest in etc. and I R0ed in Gridania. This took me to the character select screen. So I logged back in, returned to Broken Water and found my timers were about 8 seconds off. So either zoning into BW caused it or the R0ing. I'm going for the latter since I can often port to Gridania and return to BW all night and not have timers go off.