Could you please check your VDDA value using the multimeter and give that value in CYDWR -> Systems tab . Normally it will not be exactly 5V. Please let me know the results after the change.
Thank you that worked, I was using the 5V out on the programming board so I thought that would be the same as the VDDA, but measured the VDDA and it turned out to be 4.6V for this one. Again thank you it works as I want it to now.