Yes, probably. If it depended on the mute then I would look to your preamp.
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The crackling sound sounds like small tubes in the amp. If it crackles after you engage mute it is. If it doesn't then its in the preamp. Since its in both channels I'd replace the small tubes in the offending device. That might well also correct the thumping sound which I believe may be caused by a DC offset.
I have to say this. In the future, Do Not Turn Off Your Equipment. EVER. Everything lasts soooooo much longer. The components and it's internal parts (as in resistors, capacitors, ... and yes, even Tubes) all last forever if you don't have the constant demand of expansion (heating-up) and compression (cooling down) straining them. A piece of equipment left on for years will always outlast the same piece that has been turned off and on.
I learned this in a very professional recording studio I engineered at for 5 years. Nothing was ever turned off there. We had Very few equipment problems. (Mostly mikes beaten by crappy drummers).