The file was 600Mbish. It successfully uploaded via the desktop client then was later downloaded on another machine via the desktop sync thing. Later that evening it was gone. I didn't delete it (it wasn't in the recycle bin) and I confirmed it was the correct live account I was signed in as. To be clear it was still on the source machine but not the destination. No antivirus had quarantined at either end.
That by elimination would suggest that either:
1. There is a reliability limit somewhere which is unknown and unpublished or a synchronisation bug.
2. You're unaware of a process or a false positive.
I should have opened another account to test this against with the same file but to be honest if I found a bug, windows live support has been abysmal. Hell they couldn't even work out how to close my account when the close account page refused to work...