In earlier forums it was stated that patch 10.1 would resolve the inability to merge digitally signed documents.
I am using Acrobat Pro 11.0.13 and it will only allow me to put digitally signed documents into a portfolio.
Is there a fix or is this the way it just is?
That sounds absolutely correct, since merging the documents must - by definition - destroy both signatures. Signatures apply to whole files, not to individual pages. So a portfolio is your way forward.