Found the problem - any time I approved a comment, added a page, updated a page, etc. it would clear my entire supercache, even though I clearly had the options set NOT to do that.
To fix I had to tweak the source code for wp-cache-part2.php - I just disabled the entire if/then statement that starts on line 1135:
if( $super_cache_enabled) {
becomes....
if( $super_cache_enabled && 1==2 ) {
Of course this is just a band aid - hope they fix it in the next update!