You said that commercials had been removed and a one hour show was reduced to 40 minutes.
First, in my experience, 40 minutes is about average for a one hour show. I think technically it is about 42, and with the "padding" usually the show will say 40 minutes in the meta data and actually be complete. If it still too short I would take a look at the file in Schoolhouse and make sure your settings are correct. You can also check the Dtb log to see if the "less than 2 seconds" problem is still occuring, but this has been fixed for me in 188.8.131.52.
Second, what is your processing condition for processed files? It sounds like the show got processed twice if a commercialsxml was generated for a file that was already stripped of commercials. I had this problem in 184.108.40.206 with the EA update only because the metadata was not being written properly. I have not had this problem in 220.127.116.11. You can also try and see if this is occuring by looking at the Dtb log for any problems when the metadata is written. I would double check that your "already processed" files are set to "Do Nothing" and that this is the first priority.
Also, I am assuming that you have Autoskip on. That would explain why the program is skipping by itself and showing the time bar. If you intend to have autoskip off, check DVRMSSettings to change the default value. It's also possible that you accidentally hit the "UP" button (or something else if you changed the trigger) which would have turned autoskip on.