Those six hours is the reason why temporary file aren't immediately deleted when cron tasks run. If then there are many temporary file to delete, a single run isn't sufficient to delete all the files.
Wow, that sounds awful...
So maybe it's not even related to other modules, but some... cache problem somewhere? Be it browser or server-side? A Heisenbug.
It remains a complete mystery. I started enabling other modules on my clean install and boom - off it went again. Of course, removing those modules didn’t make any difference so I couldn’t...
Comments
The cron job system_cron() will delete temporary files after the max time stipulated by a constant (6 hours)
Those six hours is the reason why temporary file aren't immediately deleted when cron tasks run. If then there are many temporary file to delete, a single run isn't sufficient to delete all the files.