Could it be microphonic output tube(s)? It sounds like it the way you describe the noise and how it comes and goes. I had this problem. I found my stock 6L6 tubes to be microphonic when I bought the amp, especially on the high E string playing a G or adding vibrato to a G note. Other notes and chords seemed ok. I changed tubes to the Winged "C" SED 6L6GC tube and problem solved. Also tried the Ruby 6L6GC and they were fine as well.
Go behind your amp and listen closely where the noise is coming from when you play the offending note. If that doesn't work try taking out the output tubes then the preamp tubes one at a time until you isolate the offending tube. If its more than one tube of course then substitution would be best but before you buy new tubes try to listen then substitute.
Some tubes are just more noisy and I found the Mesa 6L6 to be pretty bad in that dept. The problem with putting non-Mesa tubes is that Boogies are fixed bias so other brand tubes will sound cold or hot depending on their spec. I found the Winged C's to be pretty solid and harmonically rich.
The Tubestore has some online reviews of various tubes that I used and found pretty helpful. Don't have to buy from them of course.
http://thetubestore.com/6l6review.html