.APL extension = aacPlus files.
This is a new supported format in Winamp 5.04
and support is provided by the new aacPlus decoder in in_mp3.dll
You will need to contact the Monkeys Audio people and tell them that their APL extension (APE List file? or whatever it stands for... sorry, I don't use APE) is now in conflict with aacPlus.
Sorry, but there's nothing we can do about it here.
can do, is remove APL from the Extension List in the MPEG Audio Decoder config (Prefs > plugins > input > in_mp3.dll > config), which should make in_ape.dll the default handler of Monkeys Audio .APL files again.