The two chips are very different in the way they work.
Make sure you have used the right current sensing resistors values for your motor.
Also make sure you have the stepping coils wired right, that is try swapping over one pair.
Finally the L298 will need a lot more supply decoupling than the L293 and the current chopping circuit will need to be laid out a lot more carefully than the L293.
Hi Mike.. thanks for the info, I forgot to mention that I was trying a two pin connection on a L298 and had based my circuit from this source: http://translate.googleusercontent.com/translate_c?hl=en&sl=es&tl=en&u=http://txapuzas.blogspot.com/2009/12/paperstepperl298n-driver-de-potencia.html&rurl=translate.google.com&usg=ALkJrhjl0u8FjoTX1wilU47EvROlEmefnA
Now, I tried switching to a four pin connection and my motor runs happily. I'm really not sure what I am missing and I really want to make this two pin configuration working.