Instead of default @note field I am using custom fields on the issue form for external and internal messages. (My Message class has "internal" boolean property) 

The fields relevant to message creation are:

msg-1@content (textarea)
msg-2@content (textarea)
@link@messages (hidden field, value is "msg1,msg2")

But only one of the newly created messages is linked (both are created). The attached patch (created against 1.4.4, should I do it against cvs trunk?) fixes the problem for me. 

See also http://thread.gmane.org/gmane.comp.bug-tracking.roundup.user/8954 for the extended diagnosis

Ksenia