Oh oh.
Our discussion got me to test it again.
I went to iCal and selected a day within the sync window that I know there is a time entry for. Nothing there.
I then went into TM, went to settings, made sure 'Sync with Calendar' is on and 'Sync on Startup' is unchecked. If I do nothing else and go back into the calendar, nothing appears on that day.
If I go into TM and press 'Sync Now', then go back to calendar, the entry is there but as the calendar refreshes, the entry gets deleted even though its within the sync period.
Whilst typing this I started to think that maybe sync with calendar needs to be on when the entry is originally created for it to stay, so I added another entry for the same day, synced, went to the calendar and both were there but both were also deleted upon the refresh. The sync period is 120 days and the entries are for about 50 days ago.