When you are using a CY8CKIT-059 the pin P3_2 has a 1µF bypass cap attached. This might cause a delay
If Bob's answer does not answer your issue, please share your project with the community.
In general, any logic clocked off of the same clock will change within a few 10's of nanoseconds from the other outputs. the exception as Bob posted is when there is different output external loading.
Thank you, I didn't notice those caps.