Silly question, but when you make a new email or reply in Mail -- is the BCC field visible? IIRC, BCC isn't enabled by default...
If you initialise the email with the other program and, instead of running your KM script, switch to Mail -- is the new email open? Is it the frontmost window in Mail? Is it even open, or is it just a new outgoing Mail in Drafts?
What is the other program? Is there the chance to add the BCC in that (I'm guessing not, or you wouldn't be asking!) or somehow get information from it about the email it has just created (eg write out the message ID to a temp file so your KM macro can refer to it)?
Failing all the above -- if there's consistent behaviour, eg the new email is always the second window back and always opens with the cursor in the content area, you might be able to do this by sending keyboard commands from KM, like "Shift-Tab four times, then paste the variable, then Tab four times".