In response to Jeff's issue - make sure your RTCM's 9.6MHz clock is GPS locked. Both Joe KC2IRV and myself have confirmed that, although using OCXO's by themselves work, they aren't perfect and move around. If you still have the little crystal in there, that will be the major source of your issues, it is nowhere near stable enough.
Fix the overlap issues to where a majority of your users are, don't worry about mobiles, it will just sound mostly like multipathing to them, if done right. Fixed stations really suffer the most in bad overlap areas.
Jesse - I use a radio base called Unilab/Stanillite KL series. They come in KL70 (can be modded to 50MHz), KL150 (for 2m), KL450 (for 70cm) and KL850. I'm pretty sure they were exclusive to the Australian market.
I've got all my audios set up the same, straight into the modulator diode. All freq response is exactly the same, and levels set the same.
The issue doesn't appear to be audio related but software related as per Tim's post earlier. My Pi does run at 100mbps though, perhaps I should be forcing that down to 10mbps as a start. I'm just not sure why changing the simulcast launch delay causes the issue, at least on the surface to be worse when that's on a per board basis back at the TX sites.