Yes, that must be the difference.
Never seen that mash schedule before. In fact I've never seen a recirculate after a sparge nor a mash of less than 1 hour - but that might just be my ignorance.
What temperature are you mashing at if a single temp or what's the mash schedule if multi step?
Personally I'd have thought 1 hour mash at 62-68 (or even 90 minutes at 62-65 for a very dry IPA) with other steps as additional time if multi step followed by draining the wort and then sparging would get you closer to the software calculated OG (although anything can be corrected by adjusting the efficiency you enter in the software to that of your system, the specific mash schedule and the brew/recipe itself).
M