1) What happened in custom when you entered USA showing AP?
-> you will be taken to the secondary inspection area since the guys upfront won't know wtf AP is.
he will ask you generic questions, if you haven't done anything illegal here in USA , you need not worry.

2) Did you have any issue with your F1 status?
-- Regardless of any other status when you come back you have to use the AP for you to be able to renew it in future.

@kopilam, If you want to get multiple entry AP, there's a field in AP application that you will need to check. Also if try to expedite the application (that will not work).
For AP applications other than multiple entries, you can write "Expedite" at the top of the application and get the AP sooner.

I advise all of you folks to read the Application instruction thoroughly. Everything you need is in the DARN INSTRUCTION.