Are you running a Managed or a Referenced Library?
A Managed Library, is the default setting, and iPhoto copies files into the iPhoto Library when Importing. The files are then stored in the Library package
A Referenced Library is when iPhoto is NOT copying the files into the iPhoto Library when importing because you made a change at iPhoto -> Preferences -> Advanced. (You unchecked the option to copy files into the Library on import) The files are then stored where ever you put them and not in the Library package. In this scenario you are responsible for the File Management.
If you're running a Managed Library then it's safe to delete the photos.
As for the importing issue:
As a Test:
Hold down the option (or alt) key and launch iPhoto. From the resulting menu select 'Create Library'
Import a few pics into this new, blank library. Is the Problem repeated there?