Once in a while motor spins fast unable to find index

The problem with my motion controller is that sometimes can not find home/index  My theory is that if home count is only one count behind the current count  motor goes forward and winds up very fast for about 360 degrees and after that motor drive gets disabled. Can I enabled it to look for home/index forward and backwards?This has happened three times for the last two weeks and it is hard to debug and troublesome to get system back in operation. I'm new to this program and every suggestion is appreciated.
Natasa

Hello,
Thank you for your input.
I am using NI 7344 board with Flex Motion 4.5 software and the problem is still here, only now is more often. I put hardware limit switch to disable the motor after it runs out of position but I still didn't figure out the root cause of this.
I have absolute encoder giving me home position and incremental encoder to do the motion, and I can not find out which one is causing motor to continue past programmed travel.
Software limit switches so far did not give me any results.
How can I get Error Monitor.flx to work?
Thanks,
Natasa 

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