1) Are you sure that pad isn't just from SCTP aligning it's chunks?
2) I'm not sure what the note in section 3.1.4 is trying to allow, but I think the message you are describing is definitely illegal.
I believe that the overall length in the 'common' header should always match that of the SCTP data chunk.
This allows M3UA data to be separated into messages when sent using (say) TCP rather than SCTP.
I suspect the note allows an implementation to add the pad (following a parameter) when it adds a new one, rather than when it adds a parameter that isn't a multiple of 4 bytes.
In any case I'd change your sending end.