Just found this and wanted to say that I had found the same thing -once I disabled wireless and mobile data the drop outs disappeared - they seemed worse originally when using the In build music player ,and better when I used Poweramp. only takes a second or two to disable/re-enable the data connections so not a big deal.
I guess if you want to match the tones for every song it would be a pain but as others have said the tone mathcing is only a starting point as each persons guitar/pickup selection will be different anyway.