Thanks guys - I appreciate all the thoughts and input.
Updating here for posterity...
I am running the latest firmware on all devices, that was definitely something I checked too.
I spoke with both Zaxcom and Sound Devices about this and neither one could offer much insight. Matt at Sound Devices said that jitter or auto frame rate detect shouldn't affect anything on the MixPre - it simply picks up whatever timecode is put into it and isn't too fussy about changes. He said it will pretty much follow along with anything. He did suggest that I record the incoming timecode onto an audio track to check and see if the timecode stream was dropping out completely at those moments where it loses connection. I did that and recorded quite a few hours of timecode and did not see any physical drops of the TC stream.
Glenn at Zax simply said that it definitely couldn't be the IFB200, but didn't elaborate. He did offhandedly mention that he didn't even remember that teh IFB200 had a timecode generator though, which was a little disconcerting.
I also have an older Denecke TS-2 slate (with the 23.98 mod) that I have been using with this rig. I've noticed however, that when I jam the Denecke from the IFB200 that I have to rejam it every 20-30 minutes because it starts drifting. I assumed that was because of an old crystal so I sent the slate back to Denecke for service. They checked it out and said the crystal was totally fine and not experiencing any drift.
So... at this point I'm forced to conclude that the timecode generator in the IFB200 is just no good; that it is just not very reliable. Like several people suggested above I am going to try clocking everything (including the IFB200) from another TC generator and see how that works out. I have a couple UltraSync One's which have dual LTC outputs, so I can send one into the MixPre and the other into the IFB200. I was hoping to avoid this solution just to keep the rig simple - this just adds one more thing in the bag and one more battery to keep track of - but if its the only way for reliable TC then I guess its worth it.
I'll update after I've run with this configuration a few times.