After checking, we found that the in the prescale file, there was a line mistakenly commented out by ":" rather than ";". For some reason, it causes T1 to be prescaled out. Correcting this typo, and all the problem seems clears (DT=8%; T1 was seen in datafiles).
PS: T12 was rebooted during debugging too.
A copy of this log entry has been emailed to: kalyan