I've had similar problem before. My E90's internal memory started to fill up with invisible files. The why I still don't know, but I solved the problem.
Simply back up you data to the mem card, reset your phone and restore.
If you want to have all your apps reinstalled after restore put all your unzipped install files in a dir on the mem card. The phone will try to install them.
Do you have emails sync to your e90? If you have, then there is a high possibility that the emails choked up your entire phone memory and the solution is to move all emails to your memory card.