It might sound silly but I think youre actually just not used to sitting that way, because I had the opposite the problem .
I used to spread my legs and sit with leg over knew, some kid told me "You sit like my dad" so I changed it, and was kind of socially pressurred into sitting feminine through my teen years.I think your body gets used to a specific habit and when it does it's comfortable, so when you change it up at first your legs are going to feel tired and out of place, I think you might have to power through it intentionally in short sessions, maybe change you leg position a little to cross the ankles instead, something like that. I think eventually if you set your mind and body to feel comfortable in that new position it will adjust.