Hey all, adding my voice to this thread as confirmation that it looks like installing KSP Community Fixes (in my case, via CKAN) appears to have solved the missing ship audio problem.
I do have BetterTimeWarp installed via CKAN, I can't confirm if that is the culprit, but assuming most people follow the general recommendations on which KSP mods to install (BTW being one of them) - if you do run into this issue, try installing KSP Community Fixes. So far so good for me, tabbing in and out of the game hasn't caused me any sound drop problems.
