There is a second possibiliy...Are you going between RS-232 and Ir devices? If so, I have found the MSC-400 can get "confused" if multiple RS-232 commands are fired from a macro too quickly before or after Ir commands.

Most of the time I see this as a problem with the slave MSC-400 hanging-up and have to reboot the slave unit. The more permanent fix was to add some delay time between the commands in the macros (0.1 seconds for instance).

I should point out that I have never had one of the units hang with just "simple" commands (Ch+ / Ch-) going out the MSC-400, so I don't think this fits your first problem (the long delay times), but might fit the description of the second problem.

EDIT:
Let me add a few more things to check (maybe this will help someone setup master/slave MSC-400s in the future, as well):

1) For the newer remotes (I know MX-6000, MX-5000 & MX-980 are "newer"), make sure the msc-400 has a RF ID >= 10 (Hex) - I use 11x. If you don't do this you will be unable to see the higher ports (above 6) when programming which port to use on the remotes (but you can still see them when programming the MSC-400s).

2) For increased reliability, make sure the Master MSC-400 and Slave MSC-400 don't have the same RF ID. I am using RF ID=12x for the slave.

The interesting thing is that if you use the same RF ID on both, the system will work for simple commands. The more interaction between the two MSC-400s there are, the less chance they will work completely. Many times having the slave with the same RF ID as the master will cause the slave to temporarily hang-up. The funny thing is that by sending the slave a few simple commands, it seems to recover. For the system to work properly different RF IDs must be used with the Master and with the Slave units. This is set under CCP in "Program" --> "Configure Home" (then select either Master or Slave MSC-400 from the tree).

3) Finally, I replaced the URC supplied 3.5mm stereo plug for RF between Master and Slave with a 1-foot long cable with 3.5mm stereo plugs. Connect Master MSC-400 RF out to Slave RF in. That seems to work properly so far. You could use Cat-6 instead using the supplied three-screw terminal connectors. In this case wire Master RF in to Slave RF in and don't wire the +5V to the slave. In any case use either the 3.5mm cable *or* the supplied connectors but not both.

Hope that helps, along with adding the proper delays. Sorry about the earlier incomplete answer.