For whom it may assist in the future, I think I got it.
The problem was that the V-drum module is set to trigger the side hits of the Hi-Hat as low notes in the drum map (D0 and I think D2). Now, most of the kits in Groove Agent are setting these notes for loops. So basically, It wasn’t just the HiHat+Kick sound, but the first note of a drum loop.
Switching to the ‘Pattent’ panel, finding the problematic loops, right-click, and mapping them to an empty note (such as D8 for example) - solved the issue.