Don't mean to be a doomsayer but in most cases you won't see anything in File manager.
In simple language there appears to be a bug with jail-broken PS3s where for one reason or another (but especially when you get within 10GB of your HDD's capacity!), when you 'delete' data, the data remains and only the 'tags' which identify that data get deleted. The PS3, to all intents and purposes then thinks that data is deleted (i.e. it becomes 'invisible'), but it is actually all still there clogging up your HDD.
Formatting is the only sure fire solution but read the multiple threads on this subject in these forums before doing so as there's more you should save/back up than you might think. Even so, odds are you may lose your trophies.
The only potential prevention is to always leave at least 10GB on your HDD and to fix permissions (and not with multiman), BEFORE you attempt to delete anything. That said, if you've alread done the deed, you can try fixing permissions anyway and see if you get any space back.
As a very long shot, why don't you try re-installing the same game but abort much earlier and then delete.
"We all agree your theory is crazy, but is it crazy enough?" - Neils Bohr