I cannot comment on perl 5.6.1 behavior, as I don't have a copy. But this matches fine on perl 5.8.0:

use utf8;
use warnings;

print "matched\n" if 'pf1ad1%/pf2%2Fad2/pdad3/pfad4/filename' =~
                                   m|^((?x-ism: [^\?]*? ))/((?x-ism: [
+^/\?]*? ))$|;
[download]

so it is possible that you have a bug in 5.6.1.

One other note: you don't need to escape '?' inside a character class. This works just as well:

use utf8;
use warnings;

print "matched\n" if 'pf1ad1%/pf2%2Fad2/pdad3/pfad4/filename' =~
                                   m|^((?x-ism: [^?]*? ))/((?x-ism: [^
+/?]*? ))$|;
[download]

-Mark