Error after update to pdf Architect 6 Professional

I have recently updated to pdf Architect 6 Professional from pdf Architect 5.
with the new version it will not allow me to save to original file name, ie, after a modification to file in pdf Architect 5 it said do you want to overwrite, which is what i need.
now with the new Architect 6 Professional i have to rename and go back and delete original file .this is surely not correct. am i doing something silly?
I have another problem that when I try to delete any file from this pdf folder it says '' The action cannot be completed because the file is open in PDF Archtect 6'' when in fact the software is not open anywhwere.