Numerous differences exist between PowerTap and Garmin computers in regards to how data is displayed. To ensure minimal differences, you should verify the wheel circumference is correctly entered into both devices and that both devices handle ride stops, pauses, and resumption the same way. Garmin computers typically measure distance (and speed, depending on setup options) based on GPS data, and does not use the auto-pause feature by default. PowerTap computers measure speed based on wheel speed and distance based on the number of wheel rotations and uses an auto-pause by default. Garmin calculates average power output without zeros, while PowerTap does not by default, but there is a setting to change this (on both Garmin and PowerTap computers).
Directions on how to change settings on the Joule can be found in the product manual.