So I've found that Rekordbox will do this if the names of the files change slightly. For instance on a Windows PC if song was labeled C:\Music\Song1.mp3 to C:\Music\song1.mp3. Notice the difference in capitalization. Same file name but Rekordbox logs it into its database differently. If you made a backup copy of the Rekordbox.xml file and it has all of your cue points and beat grids you can get back everything. Sounds like you are using the bridge so you know what I mean.
First find the files that are not importing correctly, then look at your rekordbox.xml file, and search for the filename in there. See if the filenames are different in some way (like capitalization) but still the same (I'm pretty sure they will be). You can either correct them in the iTunes folder or rename them in the rekordbox.xml (assuming the rekordbox.xml has your cues and gridpoints) and then reimport. Problem should resolve.
If you need to delete the duplicate entries let me know and ill show you a trick for doing that too.