I've noticed a reverse to padding on one of the Birmingham - Leicesters, in that it is booked to leave Water Orton 2 minutes later in the WTT than in the public timetable, however there is a 2 min path allowance at Landor Street Jn that would probably see it arrive at Water Orton 'on time' by the public TT anyway.
You're right about padding though, some of it is to regain a clockface timetable. I've noticed too in Open Train Times, there are some services that have 1-2 mins engineering allowances, however it seems to be the only train of the day that actually has an allowance but it does bring the times back to it's pattern, for example
Location A: Train 1 pass 08/01, Train 2 pass 09/01, Train 3 pass 10/00 (eng: 1)
Location B: Train 1 pass 08/03, Train 2 pass 09/03, Train 3 pass 10/03