The spec http://download.java.net/jdk8/docs/api/java/util/Base64.html says:

"MIME
... All line separators or other characters not found in the base64 alphabet table are ignored in decoding operation."

This is not so if the decoded string has to-be-ignored padding character. The following code produces an IAE:

----------------------------------------------------------------------
import java.util.Base64;

public class StartsWithPadding {
    public static void main(String[] args) {
        Base64.getMimeDecoder().decode("$=#");
    }
}
----------------------------------------------------------------------

This problem exists for all decoding methods for a MIME decoder.

Exception in thread "main" java.lang.IllegalArgumentException: Input byte array has wrong 4-byte ending unit
	at java.util.Base64$Decoder.decode0(Base64.java:1076)
	at java.util.Base64$Decoder.decode(Base64.java:695)
	at java.util.Base64$Decoder.decode(Base64.java:718)
	at StartsWithPadding.main(StartsWithPadding.java:8)


The following testcases will fail due to this issue:

api/java_util/Base64/Decoder/index.html#MimeDec_NonBase64CharsIgnored[downToZero_severalChars]
api/java_util/Base64/Decoder/index.html#MimeDec_NonBase64CharsIgnored[downToZero_twoChars]
api/java_util/Base64/Decoder/index.html#MimeDec_NonBase64CharsIgnored[validInput_ignoredSeveralCharsAtTheBeginning]
api/java_util/Base64/Decoder/index.html#MimeDec_NonBase64CharsIgnored[validInput_ignoredSeveralCharsAtTheEnd]

api/java_util/Base64/Decoder/index.html#DecodingNonValidBase64Scheme_MIME[wrapDecode_threeBase64Chars_ignoredInTheMiddle]
api/java_util/Base64/Decoder/index.html#DecodingNonValidBase64Scheme_MIME[wrapDecode_threeBase64Chars_ignoredInTheBeginning]
api/java_util/Base64/Decoder/index.html#DecodingNonValidBase64Scheme_MIME[decode_twoBase64Chars_ignoredInTheMiddle]
api/java_util/Base64/Decoder/index.html#DecodingNonValidBase64Scheme_MIME[decode_twoBase64Chars_ignoredInTheEnd]
api/java_util/Base64/Decoder/index.html#DecodingNonValidBase64Scheme_MIME[decode_twoBase64Chars_ignoredAtTheBeginning]
api/java_util/Base64/Decoder/index.html#DecodingNonValidBase64Scheme_MIME[decode_threeBase64Chars_ignoredInTheMiddle]
api/java_util/Base64/Decoder/index.html#DecodingNonValidBase64Scheme_MIME[ decode_threeBase64Chars_ignoredInTheBeginning]