I first ran into this problem when I deleted an image by mistake from the catalog (hit delete key). When I tried to reimport the image, I got the "Skip ... file already in catalog" message. The deleted image was not the Trash collection or my trash bin. The RAW file was still on the HD.
My settings: import to current location
Then I deleted the album and recreated it with the SAME name. Now, I get the message for all the images.
I opened a case with Phase but they say they can't reproduce the problem. I restarted the application several times with no fix.
I'm on Mac (Mnt Lion). Can anybody try to see if they get the same problem?