iOS6.1: Can't sync music from another computer

Previously on 5.1.1 this worked just fine, no I seem to be having problems. Has Apple updated allowances across multiple computers?

I sync and backup my phone to MacBook Pro 1. From here I maintain my iPhone and sync some photos. I sync music from MacBook Pro 2 by dragging and dropping. Manually manage music & videos is checked on both computers when iPhone is plugged in. Both MB Pros are almost the same spec and same OS.

Problem is, when I plug the iphone back into MacBook Pro 1 after adding music from MacBook Pro 2 it removes all the tracks I have synced?

Anyone managing to still do this or has something changed in iOS6.1? Or am I missing something in iTunes 10?