Are the files actually proper Dynamic Links? Sounds like you used Copy&Paste a lot and that does not create persistent information, if the comps and project files did not exist before inserting them. There is simply nothing to create a persistent reference. Everything else should not matter, but it may be possible, that premiere is using its own invisible AE instance instead of properly seeing the full UI version of AE, if AE is launched after the Premiere project already has been initialized. should not happen, but sometimes it does... What computer are you actually working on? Maybe we are straying too far into the exotic and it's a simple memory issue?
I am using a i7 Dell... a huge monster designed by moi for working with the Adobe Master Collection with 12 gb ram...so memory isn't an issue.
All the files are linked to the source so that isn't the problem either. All files are kept in the same folders and never moved or renamed. All files and clips are in both AE, Prem Pro and on the computer.
I take a single clip from my story board (file area in the project) will use it a couple of times where I trim small seconds from it to place in the timeline in Prem Pro. I will end up with, for example, two dragged clips..each from a different location from the same clip, onto the timeline. I then highlight one of the the clips that needs effects from AE and then go to my Dynamic Link and choose..replace with AE file .. this goes to my open AE project made for this video I am working on. I can then do the effects and I also make sure I re-import my "computer source" full clip to AE so it has it to reference as well as the source file in Prem Pro. I then go to the next clip and do the same which creates a second folder below in the AE project. All works well. But once in a while, when I shut down AE..first...Prem Pro says it has lost the clip info from AE and I get the placement card.
I would then open AE and sometimes the file is gone and sometimes if I then to back to my open PremPro it will apprear again...and sometimes not..then I have to redo it all over again. No matter what I always re-import the source file just be make sure I have it and it didn't get removed by the program...even thought it is still there but do this as a precaution. I am pretty convinced this might be buggie software but it could be me too and I'd like to know if this has happened to anyone else?