When the loop is in software manual, is the manual output (valve %) being set using the .SO word in the PID tag, or directly through the control variable tag? (Cross-reference the control variable tag for any locations other than the PID instruction and/or direct reference from the HMI).
Also, is the PID instruction being periodically scanned (with rung-in true) while in software manual (i.e., it is unconditional in a periodic routine, or does not have anything except the loop timer bit in a continuous routine)?