We are using C-18 column. Neither water or ACN or MeOH gives baseline stability. When hot water is run without attaching the column then base line is stable., otherwise it is problem.
Without knowing what detectors are affected, I would generally guess that's because hot water is partially degassed. Do you degass your mobile phases? Ultrasonication or with helium gas? You may want to invest in an in-line degasser for your system, they work very well. Also spend some time "tweaking" your system removing void volums.