Thanks for the heads up on this one as this seems to confirm what I found by loading an old query up in a hex editor and comparing it with the recent gpx files. There are 3 new characters right at the biggining of the text string (I presume this is the BOM you mentioned).
if you delete the 3 characters and then save the file the .gpx file works fine in memory map as normal. This text string doesn't appear on the waypoints.gpx file so this hasn't been effected in memory map.
I will report this back to geocaching.com and see what they have to say.