Firstly, download and install a later build of Eraser, to ensure that you take advantage of all the bug fixes (which, I understand, is rather a lot) since build 1376. A new 'stable' release (6.0.7) is due out very shortly. I have been beta testing this release, and it has not shown the behaviour you describe when I have attempted to find and restore files using Recuva. That said, as Joel pointed out, deleting (rather than erasing) files and then wiping free space can leave copies of data unexpectedly lying around, because of the workings of OS processes including System Restore, shadow copying and disk defragmentation. Recuva (which is freeware) is rather a good tool, in that it not only detects such files but also has an option to erase them securely, and as such it is a good complement to Eraser.
If you cannot wait for the next release, use a recent nightly build of 6.0 (not 6.1) from the Eraser downloads page, and then move on to 6.0.7 when it is released. With whatever new version you install, do a free space wipe as well as erasing files. This process will significantly reduce if not eliminate entirely the number of files that applications such as Recuva can detect and restore.
Disable System restore (and shadow copying) on any drives other than the system drive, ideally before doing the free space wipe. If you only use a single hard drive for both OS/programs and data, consider using a second hard drive or partition for your data, as this tends to make system management (including security and backups) easier to implement.
Finally, the 'nuclear' option is to make a full (system) backup of your drive using a program such as Norton Ghost or Acronis True Image on an external drive, download and burn a disk image of Darik's Boot and Nuke (DBAN), boot from the DBAN disk and run the program after disconnecting any drives you don't want 'nuked', and then restore your disk image (which itself might require a bootable disk to initiate the restore process for the system drive). While this option gives the greatest security, it is really only for those who are both technically competent and seriously paranoid.
I hope these ideas help.