ESX 4.1 is incredibly slow to reboot.
ESXi is trying to load all of the ISCSI paths during bootup and might not be able to do so right away.
To fix this, change the Scsi.UWConflictRetries from 5000 to 1.
- Open the vSphere Infrastructure Client
- Configuration Tab
- Advanced Settings
- change the Scsi.UWConflictRetriese from 1000to 80.