Mizzou - I tried increasing the program resolution to 1400x900, so I could try the larger field size as you stated. Yep, I'm seeing the same issue. Wish I could offer a solution, but I guess folks are just going to have to manually move the players around if they play in different resolutions than what I used to create the mod.
Additionally, even with the increased resolution, the ballpark edit screen remains at a fixed size. So there is no other way I could have created the mod. The good news is that once you adjust the player locations to your liking for your resolution, the players will "stick" for future games.