Hi,
I don't have a mac so if your problem is mac specific then I may not be able to help from experience.
However I suspect that your problem may be because on your new mac & editor installation you have effectively started again, whereas on your Pacemaker you have not. The databases of both need to be in sync, but your Pacemaker already has a partially filled database, of which the editor is unaware. Whilst you can sync your Pacemaker to the editor, I don't think you can sync the editor to the Pacemaker.
When you add a track to your editor, it is assigned a unique track Id (number). For a new database I would assume this starts from 1. However if you already have say 1000 tracks on your Pacemaker, numbers 1 to 1000 are already used up. Therefore trying to add another Track 1 to your Pacemaker from your new tunes, may be causing the sync process some problems.
If I were you I would probably start again with your Pacemaker. If you were to
reformat your Pacemakers's hard drive, it would effectively start off with an empty database. It doesn't matter that you already have your new tunes in your editor, just copy them to the device sync the two databases.
The disadvantage of this method is that you wil lose the tracks already on your Pacemaker, and if you do not have copies on your mac, you will have lost them. Of course you will also have to spend time re-adding those older tracks back into the editor (which will be analysed and takes time), and will also have to be sync'd (copied) with the Pacemaker.
If this doesn't work, then after reformatting you will end up with no tracks at all on your Pacemaker, leaving you worse off than before you started. Therfore If you have the disk space on your new max, before proceeding with my advice I would copy the whole of your Pacemaker's harddrive to somewhere on your mac so you have a backup. You can always copy it all back later if my advice didn't work.
Let us know how you got on.
Sox