I had this exact problem and fixed it, but for the life of me i cannot remember what the cause/solution was.
My Altium project was not super big. Altium would just always recompile for 5 seconds after i changed anything minor, unlike all my other projects which didn't do this.
Again, Sorry that i can't remember how i solved it.
But one thing i recommend trying is
1 ) save/backup your project and files.
2 ) Open a new blank sch file
3 ) Select all on your current SCH file and copy into the new file.
4 ) Repeat the same with the PCB. (select all copy to new file)
6 ) Removed the old files from the workspace by closing that project.
7 ) Close Altium and Reopen it
8 ) See if the problem still exists when opening the new files.
Since the new files had default settings and no design rules this will tel you if the issue is some non-default setting somewhere.
Then you just have to figure out what rule/setting is causing the problem.
(It may actually have been a corrupt file.)