Media Manager Driving Me Crazy

I have been using FCP for 3 years now and was an Avid & Media 100 editor for years before that.
I've just finished my first offline in FCP. I normally just digitize everything at full resolution for my edits, but my latest project used 8 hours of footage for a 52 minute program.
I finished my offline last night and today I was going through the media manager process. I've read all of the documentation and I'm no stranger to the offline/online workflow on other systems. I set Media Manager to only get what I need for the final master, deleting unused media, not capturing master clips, associated files or anything like that.
When I go to batch digitize at full resolution from the newly created project/sequence, it tells me it needs six hours of footage for my 52 minute master. Huh?
As I dissect the program,I find six short clips that are causing me problems. I can double click the clips and open them up in the viewer and it shows me in and out points and a duration of 3 seconds and 14 frames. If I control click that same clip in the timeline and highlight "Capture...", it tells me that it needs 2 hours and 47 minutes of footage for this clip. Huh?
This has been driving me insane for hours. Am I missing something? My final solution has been to delete the problem clips from the program and capture everything else.
Once the majority of the clips are in, I'll deal with my problem children later.
Has anyone else seen this? Did I do something wrong? Is the offline/online workflow always this buggy?
G5   Mac OS X (10.3.9)   FCP 5

Mark,
My archive is more just a list of our tapes, masters and original footage. Not an archive of final cut pro projects, my company has a backup and separate archival process for that.
For the tapes, I basically started with OT-1 (original tape #1) and sequentially numbered each tape. Then I also had columns for the client, job name, job number, tape number, tape format, tape number (for that specific job) and general contents comments.
Email me off list by going to my profile, my email address it there. I can send you a sample of my list. Its pretty simple, but it works for us.

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