Where to start?
Do you have the attacking unit on 'guard mode'? If you attack with a unit always turn off guard mode. One other thing that happens if you don't do this is that the men not int he 'first line' will turn around and reverse into the fight! There is a diwnside to that if the unit they are fighting routs the unit will follow them. The simplest solution is to have your main infantry line holding the enemy - so they all have 'guard mode' on but have your flanking units have guard mode off.
Next: what battle difficulty setting do you use? If you play 'VH' you will find that most units (if not all) will fight as if they were all elite/guard units (hard ot break and will fight to the end).
If you play at 'H' it should still be a challenge but units will break if you apply a fair bit of pressure.
R:TW and all mods have the ability to end battles after a certain time. It does not appear to be an option to change in the 'preferences.txt' file but it is available when you start a campaign:
In order to get units to rout you need to keep them under pressure - if you see a unit is 'wavering' then that is when you send in your cavalry unit in a charge on that unit.
CTDs: Have you read the follownig stickied/pinned thread:
http://www.twcenter.net/forums/showthread.php?t=387992
There are some inherant CTDs within R:TW - one is the reinforcement CTD. You are laying siege to a settlent and the enemy bring up an army and you fight a battle. I've forgotten if it's if you are attacked by the reliving army or not but - if you defeat but not destroy the garrison force they can't get back to the settlement and a CTD results.