My Garmin 310 XT and my bontrager Node will give hugely different results in the same session from the same HRM strap. I usually go with the Garmin but usually cross reference it with what the average of the online caloric estimators say.
When counting calories I usually try to build in or allow for some discrepancy because there is no way to be exact in how many calories you comsume or burn during exercise. I try to come as close as possible to my goal but don't sweat it if my totals are a little off either way. It usually evens out and if I'm seeing the scale move and the fat come off it's all good!