Why TS-Doctor don't intercept the commercial breaks existing in some .TS videos ?
The TS-Doctor has two methods to detect commercials but non of them are 100% perfect. That not possible at the moment.
The TS-Doctor can detect changes of the AC3 format, or for non HDTV material it can use the ComSkip tool. ComSkip has to be installed using the installer under settings/supported tools/ComSkip.