While I agree that those links are helpful in some respect, I think they miss the problem he is having. I’ve heard of this happening with some macs and even windows is seeing this pop up. The problem stems from certain necessary linkage processes being closed or frozen. I’ve seen it in cs6- current btw ae and ppro, ppro and encore, Photoshop and any of the others. Adobe opens necessary reader routines when linking, however it opens those same readers when running the program itself. The problem occurs because of sand boxing of each instance of that reader. Close the app, lose the link, even if the reader is available.
I’ve narrowed down the behavior further. When your media cache is on a drive other than the default location, it can tangle things up a bit. If two apps place media caches in different locations this is even worse. The cache is accessible by system ID (memory allocation), user ID (can execute), process ID (the program that created it has full access). Leaving caches in default locations may fix the problem on many machines (some have reported success), but I believe there is a combination of factors that can compound the problem, like the file system of where you place your files and how well it it is handled by your os.
Try running disk check and repair. Also note the formats you’re mixing (video formats). Some work well in ae but don’t pass well through dynamic link(I’ve had this issue with older 32bit codecs on 64bit machines). Some require precomposing before linking to make a preview available to premier as well as an original file.
For best result, drag clips or sequences to ae, uniquely name comps, and drag comps (precomped or not) to premiere, save ae, save premiere, close premiere, close ae. The reopen premiere and see what happens. This bypasses sandboxing of reader/communicater and uses the opened program’s reader to pass it along instead of opening a second reader in each program (I checked with process monitors), and reopening works fine (relinking too).