I've done quit a couple of upgrades from t3 4.X to 6.X but this time I have a persistent problem I cannot not understand. After doing the upgrade (all upgrade wizards ran fine), I can see in the database that the image column of tt_content has the FAL index values in it and not the file names anymore. The references to the FAL tables are ok as well. When I look at CEs like textpic, however, the image tab does not show any images. No images are shown in the FW either.
I could think of trying to fix this in TS but I want to upgrade this install to 8 and think that when the first upgrade needs such a clutch, further updates will be doomed right from the start.
[edit #1] I'm 100% sure it worked before. But now, whatever I do (update ref index, ...), sys_file_reference stays empty.
[edit #2] I now followed How to upgrade TYPO3 4.5 to 6.2 and it worked. Strange thing is that it's not really that different from how I did it all the time. Maybe it just needed me to try it 27 times :)
your problem might depend on individual contentelements. if you have individual definitions the upgrade wizard does not know, these definitions stay unchanged and as a result your 'new' images (sys_file records) are not inserted correctly.
Individual CEs might need extra care at each upgrade.
After 6.2 FAL was stable and had no big changes. I would not expect the same amount of work for further upgrades.