Mylenium has been gratefully helping with this and I thought I'd open it up. My original problem.
AE wasn't saving my linked image sequences. I would have to relink by file replacement every time I restarted project. Image files area only type of file effectd.
After many hours of testing it turns out the problem is with Media Core. I have all my effects, including AE included effects, in Media Core. None are in the AE directory. All have been deleted out. All effects are found and work, only problem is the linking thing.
I reinstalled AE and left the supplied effects in the the AE directory and disabled mediacore. All works fine now.
So, unless a obvious fix pops to mind I will have to reload all my 3rd party effects into the AE plugin directory and give up MediaCore...somthing I don't want to do. Maybe some single effects is screwing up Media Core?
any thoughts are appreciated. I hate plugin reinstalltions.
I never asked which operating system you are on, but it's beginning to sound like you are encountering a conflict with Quicktime on Mac, right? This would indeed possibly confuse AE which plugin to use until it decides to use none and offline your sequences. If so, you would have either to disable the Targa(AE).plugin found in the Format sub-folder or the ImporterQT.plugin in the (MediaCore plug-ins) folder, the latter having the disadvantage of loosing otehr QT support as well. However, neither should be necessary. The thing you probably didn't realize is the special nature of the shared MediaCore folder which is initialized differently and has a higher priority than the conventional file I/O plugins. Therefore, if you restore the original folder structure (at least for the Format plug-ins and Extensions) by placing them in the AE directory, your issues should resolve themselves.