It sometimes happens to have several different pictures that actually have the same filename (because of the camera numbering process or other things). Plogger doesn't seems to care about that and can import several pictures with the same filename : for a visitor, the pictures are present and thumbnails correct.
The problem is in the import page. Plogger doesn't refresh the "preview thumbnails" which allow to select which pictures actually import (even if, yes, i do select the picture before uploading them).
If you first import a file named img004.jpg, whatever the directory holding it is named and whatever the gallery in which it will be put, if you ever had imported a file named img004.jpg, plogger will display the preview thumbnail of the "first img004.jpg".