I have a DIY Machine that uses two motors for the Y axis, which is slaved. The problem that I'm having is that one side keeps running out by approximately 5/16th of an inch. Once it does that, it maintains that measurement. So far, I'm not noticing any regularity in the cuts I make. However, I would rather have both sides measuring the same. Any thoughts on how to address this issue? Thanks in advance.     

I have a DIY Machine that uses two motors for the Y axis, which is slaved. The problem that I'm having is that one side keeps running out by approximately 5/16th of an inch. Once it does that, it maintains that measurement. So far, I'm not noticing any regularity in the cuts I make. However, I would rather have both sides measuring the same. Any thoughts on how to address this issue? Thanks in advance.     

Have You checked the general settings? I assume You have Mach3. There is a checkbox for slave-axis following the motor that is slaved. If You have checked that box, You can not straighten the Y-axel.
Also You have to have referens-switches on both sides but separated, to have the Mach3 to do straightening.

And just to be shure, I assume that Ypu have same type of motor on both sides and that You have them configured exactly the same appart from that the slave-motor runs opposite the other motor