Well I finally chased down a timing issue with the conductor.
I sequence using LSP and the recommended audio format is MP3, at 44100Hz, constant stereo.
So I always convert my audio to that format
Where as the Conductor recommended audio format is OGG (which is the only audio format that you can load audio to the conductor)
So I sequence in LSP using the MP3 format (LSP doesn't support OGG audio), now lets say the song is 3 mins in MP3 format.
You export the sequence into conductor format. Then you have to take the MP3 file and convert it to OGG format for the audio to be loaded on to the conductor. Well it turns out that OGG re-encodes the MP3 to be very slightly longer (I think it's longer, or it could be the other way round), not by much, but enough to throw off the sequencing by about 250ms (or 1/4 of a second). Not much, but if you have singers, like I do, you can see the difference). The fix for me was to shift the sequence in LSP by 1/4 of a second to get it re-aligned.
Weird, but now I understand why some songs are slightly off at the end of the sequence.