Hi bitman,
this could have 3 reasons: (1) software, (2) hardware, (3) something completely different ;-)
ad(1)
is what you are seeing happening on the latest Manchester build? If so, have you tried rolling back to a few releases earlier (because at least the 2 recent ones had optimizations included also to track solo functionality) ... so it might be worth checking whether this is software or hardware induced ...
ad(2)
soloed or not, disk load should be the same ... so i would not suspect hardware in the first place but it could be that you are at the limit with HD performance and just a little extra required from the software causes the inability to read all. however, this should be scalable i.e. archive 5%, 10%, 20% of tracks and see when audio drop out goes away ...
ad(3) something complete different ... the Monty-Pythonesque kind of problems ... the ones that do not make sense until you figure them out months later ... e.g. I got audio drop-outs exactly 59 seconds after the start of any song (actually as severe as an audio interface crash) and it took me a long time to realize that I for some stupid reason enabled "always echo current MIDI track" which caused a MIDI loop that took exactly 59 sec to overload all buffers ... took me 1.5 months to figure out. i'm not saying it's the same in your situation, but something done lately that you do not suspect in the first place could be causing all these troubles ...