I've been looking inside the app created with pd and it seems that I've fixed the problem.
I opened the file "APP/Contents/org.puredata.pd.plist" and saw that PD was trying to open my patch (that was in the "extra" folder, inside it's own folder, the one from which I wanted the app to be created from) from a wrong location. For some reason, PD was expecting the patch and it's containing folder to be named the same. In this case, it was asking to open a file located in a folder that didn't exist (a folder with the patch's name). I simply changed the wrong folder's name for the write one and everything seems to work fine. Any ideas about this? Am I missing something?
Ignacio