LEAP contains a number of default GWP values (for 20-, 100- and 500-year residence times) for all major GHGs, which include different sets of GWP values taken from different IPCC Assessment Reports (ARs). For AR5, you may further select whether the GWP values include or exclude changes resulting from climate feedbacks. You may select a single AR and apply those GWP values throughout your model, or if you wish, you may select different ARs for different scenarios. This is done through the
Scenario Manager.
Using default effects and their global warming potentials (I emphasize *default*, since these are all editable by users, and I can't say whether you may have changed any of these values or names without looking at your model), LEAP defines a pollutant called "Methane Biogenic" with a 100-year GWP of 28, using IPCC AR5 values without climate feedbacks. It also defines a pollutant called "Methane" with a 100-year GWP of 29.8 using IPCC AR5 values *with* climate feedbacks.
Are you certain that all of your scenarios use GWP values from the same IPCC AR? And, are you certain that you are not comparing two different methane branches, perhaps one that is "Methane" and another that is "Methane Biogenic"?