Thank you for your comprehensive description of this strange behaviour. If you have specific questions you may send an email to firstname.lastname@example.org, since in the forum further inquiries could not be stated easily.
Referring to your problem, this is the first case of this kind we heard of. FlexPro stores it project databases (.FPD files) as compound files, and uses no network specific means (if no network license is used). Can you rule out any interaction maybe with anti-virus scanner and/or firewall trying to check for the integrity of the .FPD file in the AD case?
Huge project databases can also be stored as a structure of files and folders instead of a single compound file. You may test, if this changes the strange behaviour while loading the database.