I am not 100% sure that this is what it is but it is what I am thinking. Here is what is happening. I have an Industrial CNC A404 running mach 3. I do not have an auto tool changer. I cut my parts using a 3/8 bit and then I change to my 1/8 bit to drill holes and run the new file. Every time I do that my Y axis seems to be off about 1/8- 3/16. It is almost like after it cuts everything it doesn't come back to the exact same spot I started at so it ends up starting from a slightly different point. This is resulting in holes being drilled in the rong spot. The X axis seems fine though. It is only the Y. I have used a dial indicator and calibrated the machine with the steps per inch. It was pretty much dead on. The machine is about 6 months old and I have had this problem pretty much from day 1. Any suggestions.

Sounds like it's losing position in the Y axis. Try reducing the Y axis acceleration and velocity by 25% and see if it helps.

Also, make sure that it's not mechanical, making sure all setscrews, nuts and volts are tight.

It was at 350 and 12. Now I am at i think 262.5 and 9. I have some stuff to run later. I will report back and let you know. Also the X is at 400 and 12. Should that be reduced to make it comparable to the Y?