Not sure if there is a way to fix this issue, or if this is just one of TRIMs lovely eccentricities.
There appears to be discrepancies in the order of adding notes to a record in TRIM. For all our record types we have our note settings as 'When adding notes to a Record, insert the text Only at Top" which is hunky dory, except for when a user checks in a new revision and adds notes in the 'Comments' field of the Check In window. The Notes will then be placed at the bottom of the notes – making the notes out of order and obviously causing confusion. Does anybody out there in TRIMland know of a way to rectify this issue in TRIM that I'm just not aware of?