LostInBatCountry
I used to play TripplePlay2000 on the PS1 back in the day, and as far as I'm concerned its the only baseball game every made that isn't terrible. I have the MLB 2K10 and the MLB The Show series for PS3, and they are ridiculously hard when it comes to scoring runs. I think its more about patients, as the newer games are designed for realism.. and baseball can test the patients of any wholehearted athlete.

Steven
I can't say I've had the same problem. Mostly it's about patience. Don't expect to score a run every time you get on base. Try sticking to one base per hit until you start to get the hang of it, then you'll be able to predict when you can run further. I don't know what game you're playing, so I can't really help you further than that.