Hmm... well here are some ideas..
1. Check the FR user groups to see if anyone else using the revolution has had issues with the clock send. The synth section is analog, but the sequencer is still digital and it shouldn't be that weird. My experience w/FR hardware is very limited but you never know there could be an update that solves the problem.
2. If you are daisy chaining midi throughputs to get the clock everywhere it needs to go, this can sometimes add latency and cause other types of screwiness with the midi signal. See if you can get a different result by changing midi connections, taking devices out of the chain etc. These days if I'm working with a setup that requires chaining more than one device on a throughput I just use a dual-out through box or an MTP as a patchbay and run it all in parallel. Timing's great.
BTW you don't have to fiddle with cables to change sync on stage anymore. You just need 200 bux for a MUNGO SYNC:
http://home.netspeed.com.au/aistorm/sync2.html
You could also just try using tap tempo and forget about midi sync altogether I suppose.
EDIT: It could be an MPC problem. I have noticed a few complaints about problems using the 1000 in external sync mode. I only use external when I'm doing weird tempo sequencing experiments -- basically messing stuff up -- so I wouldn't really notice a problem like that. Otherwise MPC is always master.