I run 2-5 clients on the same computer, and I was running into the same problem with apparently random disconnects. After hunting around the official WoW boards, I found a known bug with /follow.

A few players were reporting that characters /following a non-mobile avatar will disconnect. Basically, if Character #2 is /following Character #1, and #1 stops moving to fight, loot, etc, there is a chance that #2 will disconnect if it is left on /follow. That's why your primary box will never disconnect this way.

It also seemed more common to disconnect if I tried to use a skill from a stationary position while on /follow.

To circumvent the bug, I make a point to move and spread out my characters once my main has stopped moving, and only resume /follow when I'm on the move again. Once I started doing this, the disconnects stopped.

When the WoW forums are back up I'll link to the Bug Report. The QA rep said they found the problem and were working on a fix, but I haven't checked to see if it was fixed in 2.2. Hopefully it's now a non-issue.