Which to shut down first.. AE or PremPro when linked

Hi,
I have PremProCS4 and it has linked files to AE CS4..both open and all is well. Effects are in and looking great. I've worked in this same project many times.   Now when I close AE first Prem Pro has a fit and looses the links.  I reopen AE and have to bring in the missing clips again.  These are brought in from my computer files too since AE needs the computer ref as well as the clip in PremPro.
This doesn't happen all the time so I am perplexed.  Is there a formula I need to follow in order to shut down these two programs and not loose the links?  I save on a regular bases too.
Thanks in advance.

Hi Mylenium,
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?
Thanks

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       Keywords 0x8000000000000002
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       EventRecordID 8270
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       [ ThreadID]  8
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      BugcheckParameter4 0x0
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    _AC2 = 0K            
    _AC3 = 0K            
    _AC4 = 0K            
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