I have the same problem, although I haven't installed the speedball upgrade yet. Only occurs on startup and the volume pot doesn't affect the crackling whatsoever. It can also get pretty loud for a few seconds and then it goes away, usually until I turn it on again the next time. I've had mine for about 6 months and this only started about 2 months ago. Sounds like our issues may be the same. At this point I assume it's a grounding issue somewhere in the chain, but some help/tests to check this would be really useful.
In the meantime I'm going to check the grounds and will let you know if I see anything...
Update:
So I just reseated both tubes a few times and noticed that the cracking on startup has diminished if not disappeared. However, I still notice intermittent crackling during playback, but with less intensity than before. Having gone through some other posts I am wondering if this is a tube issue and not wiring. However, I also notice that if I play with the headphone jack it seems to effect the crackling sound. Often I'll take it out and reinsert and then I'll get a loud crackling for a few seconds and then it seems to resolve. At this point I'm kind of baffled as to the genesis of this crackling is...
Anyone??