<<<I still have 100's of files.>>>
That's probably not true. You have thousands of files. It used to be that if Audacity 1.2 went into the mud, so did the show. The developers realized this kind of sucked, so they and some other volunteers developed tools to recover whatever they could from the pile of debris.
Crash Recovery
http://audacityteam.org/wiki/index.php? ... shRecovery
You don't really want big capture segments. The bigger they are, the worse the problems are of drive management and the worse off you are if you happen to need to rescue a show. If everything comes out OK, you will only be missing the end few seconds of your current show, not the end five minutes.
Regular users of the program are horrified when people try to record for days instead of hours or minutes. Your machine has to be in perfect order with no unstable conditions and huge amounts of free and defragmented hard drive space. Your machine didn't do one or more of those things right.
One of the ways you can insure success is to run a good memory checker overnight. Unstable machines won't make it that far. Microsoft makes a good free one.
http://oca.microsoft.com/en/windiag.asp
How bad was it the last time you defragmented your hard drive? Lots of red lines in the fragmentation map?
Koz