I had a similair issue, don't know if its going to help, but my situation and solution were as follows:
- All tracks routed to several busses
- Busses routed to mixbus
- Mixbus router to main out
- Lots of compressor usage (Fabfilter pro c2) for generla compression and sidechaining of pads and bass
- Put fabfilter Pro-L on mixbus (limiter)
- Introduced quite some latency (ca. 60ms)
- All previously created sidechaining out of wack
- Issue does not occur with Pro-L limited disables
- Issue does not occur with Fabfilter Pro-c2 or Pro-q3 (EQ)
- Issue also doenst occur when using Studio one stock limiter on mixbus
- Moved fabfilter pro-L limiter to main-out (master) channel
- No more weird timing in side chaining
For me it was basically the limiter introducing too much delay on the signal chain and not being compensated, however it was compensated on the main out for some reason.
Hope this gives a different persepective.