Could you post two files of the sounds by themselves, then one more of them together?
It's hard to make any judgements without audio. What you are hearing as mud sounds like it wouldn't be a phase issue at all...More often than not phase is only an issue when the sounds become hollow. Not to say phase can't screw the low end in ways that don't make it hollow, but I have a hunch that you aren't dealing with a phase issue.
Until we get examples, try nudging either your bass or synth slightly. Phase is a timing issue. If it's really a phase issue the sounds will dramatically change as you nudge them.