Figured it out – but it wasn’t obvious.
I had a AE comp and files that were working on drive A. I needed to update and revise the project file but didn’t want to loose the previous version. So I collected the file to another folder on Drive B. AE completed the collection. I ejected Drive A, then double-clicked the collected AE project file on drive B and it messaged 168 files missing. So I relinked one of the files that were missing, but none of the other files re-linked. It seems like previous versions before CS5 just did this with no problems.
I re-set prefs and tried again – same problem.
So – I moved all the footage files out of the collected footage folder up one level into where the AE project file was located, re-opened the file, re-linked one missing file and viola – all the files re-linked.
It appears that the footage needs to be in the same folder as the project file, but the default file structure for a collected file is not arranged that way, so has something changed or is this a bug?
Like I said it seems that previous versions of AE were not that picky of where the source files were.
CS5 AE 10.0.1.19 on a 2X2.93 GHz Quad Core Mac running 10.6.6