Since this problem occurred, have you Reset the iPod?
http://support.apple.com/kb/HT1320
If that does not help. You can also try doing a Restore, in iTunes from the iPod's Summary tab. This will erase the iPod, reinstall the latest software, and set it to default settings.
the nano is at rest on a table and plugged in to a bose stereo system
In that case, does this problem ever happen when it is connected to regular headphones (not connected to the Bose system). The nano can accept various commands from the headphones cord (when a cord that has the remote control buttons is connected), so maybe the Bose unit is somehow sending a signal that is interpreted as a command to pause workout.
the fitness voiceover tell me how much time has elapsed
Does that audible update happen automatically? You don't have to touch the nano to make it say the elapsed time?