Not sure who is to blame here - best to file a bug on iCal.
iCal will be using AppleScript to send the text of the alarm via a mail message.
The body of email messages should not use a single LF (0A) to represent a carriage return - because that signifies the end of the body. New Lines should be CR LF (0D 0A) - I think....
However the Applescript used in iCal just set's the body of the message as the contents of your alarm - so if you have a new line in your notes of your alarm then it is dumped into the body of the mail.
Strangely I can't find an Eudora script in the iCal Package - so I'm not sure how you could fix it.