This happened to my wife a couple of months ago. We had gone to HKG on business, then she went on to SIN on Singapore Air and I returned to YYZ on AC.
Upon checking-in in HKG she was told that this was an "Asia internal" flight and she was only allowed 1 suitcase weighing whatever (less than the AC TPAC allowance). We went to see the AC agent who phoned over and got her checked-in with the AC allowance.
She was told that when checking in at Changi for the return journey, to show her entire itinerary from both Singapore Air and AC, so the agent there would be able to see that it was one TPAC journey. She did that and everything worked out fine.

PS First post, have been lurking for a few weeks, and already got a lot of useful info - thanks all. Both of us just made P so are babes when it comes to FF issues.