Merged Clips Appear Off Line Yet Are Successfully Linked In CS 5.5

Hi there. I just migrated a feature documentary from an edit suite in a local production company to my home. We're using Adobe Production Premium CS 5.5, I tried to migrate the project using the Project Manager function of premiere. But no matter what combination of options I tried it failed everytime. Huge pain!
Anyway, the whole thing is nearly up and running again - but there is a problem with some of the merged clips. We were shooting on DSLRs, with a Zoom H4N dual audio system. Dual Eyes was then used to synch the clips. Which were then merged with the relevant video files in the various relevant bins.
Here lies the problem, obviously I had to go and relink all the media files. Grand job. Thought I was all done but then I noticed, that when I was linking "merged clips" they weren't coming up properly in the sequences. Like, they were there in the bins. They would appear if double clicked in the source monitor. You could even do an old "in and out" and drag your selection into the sequence, and all the extra Dual Eyes audio synchs would be there and ready for use. But, the ones that were already in the time line were not picking up anything, they were just off line.
I find this stuff hard to explain so attached is a screen grab and some explanation below.
A - Shows the panels with the media successfully linked.
B - Shows it double clicked and opened in the source monitor.
C - Shows where it should be in the time line. But its not linking.

Just tried moving the source files and relinking - no luck what so ever.
Any other ideas?

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