Hmmm, are you using a y-adapter or just a single connection?
If it's just a single connection, I'd try troubling shooting the LFE RCA input. A couple of times I have seen loose inputs that can cause an intermittent problem like you are describing. I'd try either the left or right inputs (doesn't matter which one) to see if that takes care of the issue.
Also a y-adapter is not a bad idea if you aren't using one already as it increases the signal strength to the sub.
Jason Hicks
Aperion Audio Guru