Wow, that's very strange! I have my Suunto running watch syncing to Strava via the Suunto Movescount app - there are always pauses in the data (have to stop for traffic!), but they don't seem to distort my distance and pace data at all (in fact, Strava just shows "moving time" separate from the total time of the activity. Perhaps an e-mail to Strava support would be in order.
Oh - thinking about this - I don't know if this is the case with cycling data, but for running data, pauses DO get included in the way you describe if the activity is "tagged" as a race (otherwise, only the moving time is used to calculate pace). If there's something similar for cycling, perhaps you can toggle it off to get Strava to "ignore" your coffee breaks?
