Now that I can see the bigger picture, I think I know what the source of the issue might be...
The first issues is the extra innings channel. They are not like regular channels they go on and off line and such and really screw with manual recordings. As such, because their guide data is different, people have posted a few weird quirks over the years sometimes on these channels with manual recordings. I don't think it will ever change to be honest. (There's an entire debate in there on how manual recordings work, and let's just say they don't work like I and you think they really should, but since I never use them I don't really find it an issue myself.)
You should also get the RSN channel that has the game while the game is on, I'd suggest figuring out what channel that is and setting your recording for that channel, but would need to make sure its on. That could fix the issue. I suggest padding it for at least an hour anyway.
Personally I record a ton of sports and I always pad all my sports for three hours, I don't want to miss ot.
Directv TiVo never could record properly with wishlists for sports, so I found them far far inferior since it failed one of the most important functions in the world to me, and yet every other DVR I have ever had has done it superbly. It's all in how you use them.
The best solution is if you can get an upgrade to a genie for free. Five tuners and twice the recording space, you will never have to worry about conflicts, and will never have to worry about letting it record the entire six hours. Also they have a fantastic sports search and auto record system to grab any teams games similar to how a whish list was supposed to work for tivos. Only DirecTVs works. Oh, and genies are faster than your current DVR too.