Problems with JavaMail 1.3.3
I'm not sure exactly what's happening, but it appears that on some platforms, under some circumstances, Base64 decoding, or something underlying it, in JavaMail 1.3.3 breaks horribly and produces data with lots of extra bytes of the value 0x00 and 0xff. The upshot of this is that messages containing Base64 encoded data, such as S/MIME messages will no longer work as the data stream containing the encoded message has become corrupted.
If you have trouble running the S/MIME examples there is a good chance you are on one of those platforms. In this case I would recommend moving back to 1.3.2 until the problems in 1.3.3 are fixed.