I have enabled a custom schedule state field that would come after "Accepted". It does not appear that the Percent Done by user story count takes the custom state into consideration.
Thanks for contacting CA Agile Central Customer Support. I am very sorry to hear you are encountering this issue. If your US set the custom schedule state that after "Accepted". It should also count in "% Done by story count".
I will create a support case for this issue and check with you the detail from it.
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