I've noticed that after saving, closing, and re-opening a Song file, Pro EQ's latency reporting seems to break.
In parallel chains, I will sometimes use Pro EQ for pre-emphasis and post-emphasis curves to keep most of the low end from hitting something like Waves CLA-76 (which has no internal sidechain HPF) too hard. This will work great, until I come back to the Song file. Upon re-opening the Song, I will immediately hear nasty comb filtering on the buss or channel that has the parallel chain in it. Turning off one Pro EQ instance changes the filtering somewhat, and turning off the only remaining instance removes the comb filtering entirely. Likewise, turning off High Quality mode on one Pro EQ instance changes the filtering somewhat, and turning off High Quality mode on the only remaining instance removes the comb filtering entirely.
As far as I can tell, this means the slight latency induced by High Quality mode in Pro EQ is no longer reported correctly (and thereby no longer compensated) after saving, closing, and re-opening a Song. This is not apparent in a series insert chain, because that single channel will be milliseconds out of time, and no others, but it is very apparent in a parallel insert chain, because one half of the mix will be milliseconds off of the other half.