Are you using powerd? It seems that your CPU was throttled before the
reboot, because of low load and when rebooting got stuck there. Try to
deactivate powerd and see weather this still occurs. If so, you can put
something into rc.shutdown that stops powerd and sets your cpu back to
full speed.
Often when I reboot my system it restarts with the wrong CPU
frequency:
Apr 7 22:24:53 xor kernel: FreeBSD 6.1-PRERELEASE #19: Tue Mar 28 15:15:20 EST
2006
Apr 7 22:24:53 xor kernel: ACPI APIC Table: AMD-K8 AWRDACPI
Apr 7 22:24:53 xor kernel: CPU: AMD Athlon(tm) 64 Processor 2200+ (797.73-MHz