50/50 making odd noises

Hey guys. I'm new to the board, but I've been reading around, and you guys seems pretty knowledgeable. I need some help. I recently bought a 50/50 to go with the triaxis that I've had for a year or so. I love the tones I'm getting out of that combination.
The problem is: When on high power, the 50/50 causes my speakers to sound like they're being turned off and on (boom boom) over and over. Eventually it fades away, but it frequently returns. I called the mesa/boogie reps in CA, and they said that it's a possibility that changing tubes would fix it, but it doesn't sound like the tubes need replacing, and I'd hate to invest in new tubes on the off-chance that it'll fix my problem. The amp sounds much better in High Power mode, so this is a pretty serious issue.
Help a brother out,
Carlos

I would listen to the guys at Mesa, they know what they're talking about. I've got a 50/50 and the only problems I've had have been power tubes.

I do believe they know what they are talking about; but if I'm describing the problem accurately, does it make sense that tubes alone would cause this?