I am also using Backup Exec 12.5 for Windows Servers and am running into the same problem. Inventory Library Jobs pop up every day and stay queued. If I try to cancel the Inventory job, the Job status changes to Cancel Pending, but it will not actually cancel - it just sits there. The only way I have been able to clear the job is to restart the BE services.
I am using an Exabyte LTO 1x7 Autoloader, with the latest firmware from Exabyte. I also suspected it may have been an issue with the Autoloader and have contacted Exabyte (now Tandberg) becase I was also unable to unlock the Autoloader to swap the tapes. From BE, any Unlock jobs would do the same thing as the Inventory job does now. They ran me through a series of tests and eventually told me that Backup Exec is maintaining the locks and that the only way to swap the tapes when that happened was to power off the Autoloader > remove the SCSI cable > power it back on > swap the tapes, power t off > reattach the SCSI cable > power it back on. (I am currently looking at a different Autoloader for various reasons, one is the hassle of this problem).
What is weird is that the unit also responds great for our differential (weekday) duplicate backup to tape jobs, but the full (weekend) backup to tape jobs are always a hassle. It will fail when writing to tape and will not work unless I restart the services and then manually restart the job - then it works just fine. I have the latest live updates. If anyone is ninja with logs or can lend a suggestion it would be most appreciated as sporadic issues are the pits...