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When I power up the table and run the reference all the Z then Y react in a timely manner, but the X (last in my string) take a verys long time and after it homes the run indicator blinks for a long time before it finishes the reference function. Is there a setting where I can change this to shorten up the reference time??

The reference should happen relatively fast, there should not be a huge time delay between the axes running to the reference position.
So, it sounds abnormal if you experiencing a huge delay between them. What time are we talking about? Approximately in seconds?

Thanks for the reply
Ok I have the reference starting with Z then Y then X. it starts the Z in about 5 seconds, then the Y about 5 to 10 seconds. To get the X is about 25 to 30 seconds and for the run indicator to stop blinking another 30 to 40 seconds. I never saw this with Mach 3, the whole sequences was maybe 25 seconds unless the table as at the far reaches of its trave. When I start the sequence now the axis are not more the 10 inches max.

I never seen this with the UCCNC either with any versions.
Your computer might be too slow, the referencing requires lots of syncronisation between the software and the motion controller, it does several steps to make sure everything happens properly. Normally one syncronisation should not take more than a few tens of milliseconds, but if the computer is not up to the task, if it is too slow then it could take more time.
However if it takes seconds then it is really problematic. Can you test it with a different computer?

Please, upload your profile to check. Maybe, there is a combination of too slow homing speeds and a homing back off.

Just out of interest, what is you back off speed set to?

thanks for the replies I will look over those thing, I will send the profile soom.

Ok I worked with it and found that the "Homing speed up and down" were low, after entering 100 in the X and Y axis setting. Then the time between the Y and X motion reduced and the time after X was home and the run button stop flashing, was also reduced. The reference action for the 3 axis is now a nice smooth and timely manner and what I expected.
Thanks for the replies.