For color film I use PE's recommendation of a 30 second pre-soak, including a 10 second drain time, then repeating with a second 30 second pre-soak. This is to get the film up to temperature before the developer. Kodak recommends against any pre-soak with color film, but I just can't bring myself to skip it completely.

As far as your issues go, I'm just spitballing ideas.