if I have Classic running on my 10.1.1 iMac I can't shutdown or rebot until I force quit Classic (9.2.1). It has not always been like this, it came with 10.1/9.2.1 or 10.1.1.
the only time i encountered this, i ran a disk repair utility and fixed the volume structures and all has been fine since. Diskwarrior and techtoolpro are both good for this.