Media Manager grabbing wrong TC

I've been trying to recapture an hour long sequence at an uncompressed AJA kona resolution using only the media used in the time line.
I have already been sucessful with two other sequences but there are two that are giving me a fit.
The first one won't even run through media manager and gives me a general error 34 message.
The second one will run through media manager but after it recaptures everything part of the sequence has all the wrong time codes for only one tape.
However, the first part of the sequence is fine.
It also seems to be capturing more media than it has in the time line. I have checked my media manager settings several times against what the user manual suggests and still get the same results. I figure the sequence is bad, but then why is the lower resolution version still correct?
I am very puzzled here.
Jaustin

The original video is 1080psf 23.98 10bit uncompressed 4:2:2 (captured DIRECTLY to hard drive from a sony cineAlta
I had 5 hours of footage. i made my edit and locked my picture...
now i wan't to make a COPY of the locked picture and ONLY the media used in the timeline (plus 1 second handles).
when selecting the appropriate options in media manager, the "modified" storage size stays exactly the same as the original....even when checking off "delete unused media"
I am familiar with media manager, it appears to be malfunctioning...because NO options, checked on or off, seem to make the modified size change!
thanks in advance for input.

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    Occam's Razor nearly always applies when troubleshooting technology issues!
    If anyone has been helpful to you, please show your appreciation by clicking the button inside of their post. Please click here and read, along with the threads to which it links, for helpful information to guide you as you proceed. I always recommend that you treat your BlackBerry like any other computing device, including using a regular backup schedule...click here for an article with instructions.
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