So, I'm having this weird thing where I'll open Premiere and After Effects and then choose the linked projects from each start page to load them up. Then, when I right click on a comp in my Premiere timeline and click "Edit original" to take me to the comp in After Effects...AE reloads the same project as if I was in a different project...then the same project shows up twice in "Open recent" with a shorter and a longer path...but it's the same file. I don't know if this might also be related to the other issue I have with dynamic links, which is when I make a change to a comp and save the AE project, multiple comps linked in Premiere go offline and I have to relink them.
Without more specific info about your system, the structure of the AE and PR projects, where files are stored and so on nobody can realyl tell you much. To me it seems there's simply an issue with resolving aliases/ symlinks which may have to do with how volumes and folders are mnamed and mounted in the file system.