ok i have more of an idea of what's going on.

first of all, when you choose to scan the particular recording that has no detection done on it yet by saying yes, it begins processing the file in the background. on a fastish system (for instance i only have a celeron d 2.93ghz) the file should be scanned by the time you hit the first set of commercials. the problem is that the plugin does not recognize the newly created xml file until you stop and restart playback (must check when you first start loading). this would confirm why when you go back to it that it works.

this means that:

a) commskip addin is working (up, down, left, right are responding)
b) SA is working because you have an xml
c) filewatcher seems to the culprit, is it running as a process when you open the task manager? have you read the wiki on dvrmstoolbox? it tells you how to set it up. if not setup properly it will not work at all.

also, i'll say it now cause i'll probably forget later on, you owe a n00b some help next time you see one asking for help and you know the answer.