Hello i thought i would post this in case someone else is struggling to get WinAPE to recognise their 360 Controller.
The solution for me was to go into the "Game Controller" Settings of Windows click on the Advanced Button and Select the 360 Controller as the Default controller.
My machine also has an air mouse connected for my HTPC use and this was recognised as a controller and set as default once default changed to 360 controller everything worked again in WinAPE.
Took me two frustrating days to work this out may help some newbie like myself.
Is it letting you use the D-pad though or are you stuck using the left analog stick?
Left analog stick only unfortunately. But still happy with this solution over the keyboard.
Ah ok. I've switched emulators for the meantime to Sugarbox just cos it let me use the d-pad of my Dual Shock 4 rather than the left stick. CPC game feel much more responsive with proper digital controls. :)