Ugh, we are having the same issue with just select clients.  Some have gone through and I can't find how the rejected ones are any different than the ones that have been accepted. 

Sorry, not answer for you, but wanted to let you know you are not alone!

Lacerte tech support researched the issue and responded that if a federal extension was filed and no tax is due to PA, then PA does not require an extension to be filed.  While this is true I believe the Lacerte program allows for the filing of extensions if you so choose.  Since the e file wizard passes validation ,Lacerte is allowing, but PA is rejecting since an extension is not required.  I guess PA wins this battle.

I filed a manual extension

I understand what you are saying; however I've had PA accept the extension for several clients that meet the conditions described, while it rejects if for others?   Just and FYI on the subject. 

We are also filing manual extensions!