Such is the beast that for multi-platform programs, you end up creating the app as a lowest common denominator, with plenty of overhead code to prevent it falling over on variants of the operating systems. There are many variants of Unix, Linux, and Windows, and some variants file systems work differently, causing problems. I join the chorus in highly recommending a File::Spec or similar cross-platform filehandling solution, so you don't end up with workarounds for OS variants throughout your code. Then as long as you use the module properly, your app will run on many OS variants, current or future.
Mind you in OSX you could instead create an ActionScript action instead, or your app could be made into a service, which could make things nicer, but unfortunatelly not portable to other OSes.
Maybe (or maybe not) you'd be better off having a gui/web interface instead of drag'n'drop to console. Using a console in the first place assumes a certain level of user knowledge, and you might just be better off to get them to specify path instead of introducing the drag'n'drop to console thing into it.
if you want your project to succeed, you will need to think about your application audience closely, to avoid disappointment. whether you're a programmer/software-engineer or not.
all the best in your project. you might possibly be interested in a freshmeat project called "Sally", so i mention it.