As long as it doesn't take foreeeeever to start up, I think shutting it down is the best solution. You could also just leave it on during the day without sleep (just turn the monitor off) and then shut it down at night if you are going to be back and forth from the computer throughout the day.

Hard drive problems can create weird behaviors from a computer. I once had a hard drive go "poof!" but only after it created massive amounts of weird graphics problems. I thought it was my graphics card, so I replaced it. I thought it was the drivers, so I dumped and replaced them. In the end, the HD had a fatal error - but it didn't manifest that way.

(Which is not to say your HD has a fatal error - my problem was a LOT worse than yours - but just that HDs can do weird things.)