Well, in 1992 and 1993 the Jays both outperformed their run differential by a few games. Not the team's fault that you guys were born too late to witness those great years.
Check the all-time franchise stats the Jays' W-L record is 3,383-3,458 despite scoring 31,599 runs and giving up 31,485 so it has been a problem throughout the team's existence. Must be the weather.