Common mistake. Let's say you have records A, B, and C. When you omit record A, you land on the next record (B). Your script then goes to the next record (C), without even looking at the checkbox of B.
The solution is:
Go to Record/Request/Page [Next; Exit after last]
Yes, all scripting is done in Scriptmaker (now called "Manage Scripts"). You can print a script to PDF when you want to copy and paste it as text.
Ahhh....nice. I didn't realize that "omit record" itself actually takes you to the next record. Good call. It works now beautifully. Thanks!
You don't have to loop through every record, checking each one individually. This is what "Find Mode" is for.
Enter Find Mode 
Set Field [SpecialOrders::complete; 1]
Constrain Found Set 
Does that work...?