I'll take a shot since you haven't gotten an answer. Apex reads the statements top to bottom, and acts on the last true statement. My guess is WTRLV1 is keeping the skimmer running since it's after your pH command. I would write it like this:
Fallback Off
Set On
If Output Return = OFF Then OFF
If pH is > 8.45 then OFF
If WTRLV1 Closed Then OFF
Defer 010:00 Then ON
If Power Apex Off 002 Then OFF
Last line keeps the skimmer off for two minutes if there is a power outage, so the sump level can stabilize if necessary.