I know exactly what it is...........
I spoke to Mesa about an "Upgrade" I head about and they said all RK's made before 2005 probably need this upgrade (or fix).
I asked him what the upgrade was for and I was told that the RK has a couple of LDR's inside that when you run channels 3 & 4 for 20 - 45 minutes, those LDR's will over heat and cause a volume drop in the amp. Some times it is a sudden drop, sometimes it is a tremolo effect, and sometimes it just looses gain and sounds almost clean and real thin.
I also asked if I should wait and see if this problem will occur in my amp or go ahead and get it fixed and he said "It will occur eventually" and knowing Murphy's Law, it will happen at the biggest show of the year.
Luckily my RK is still under warranty and I have it scheduled to go in to a local mesa repair guy next week.
As far as the crackeling noise?? That may be related, but it also sounds like a bad preamp tube or guitar cable. Take a pencil and tap the preamp tubes (with the amp on) and see if one is more microphonic than the rest and if it is, I'd change it and see if that helps. My Triple has a bad V1 preamp tube that made it sound like what you described. If you cant tell by tapping on it, get one new tube and do the sawp out/replace trick with each tube until you find the bad one. But if it's related to the first problem, then a new tube wont help.
You amp should be under warranty, even if you arent the original owner if you can get a copy of the reciept you can get it fixed for free.
* Bad news is you'll be without it for a week or so
* Good news is it's a very simple, easy to fix problem and it should be free to fix.
PS, my serial number is 001818 and it left the factory in August of 2004 if this helps determine how old yours is.