Firstly Thanks for the great contribute Chris,
Secondly i got the same problem with the pdf not attach to email when HTML Email is set to true, for the last 2 days i was looking thru the checkout_process.php cluelessly cos i am noob to php script hee hee.
I found out the reason Why it won't attach the pdf, for my case. below is for your ref
The problem is with
But still i can't get it to work, only get it in 2 emails. 1 attached pdf, other 1 is the Fancier_invoice_6.2_Fixed_2007 contribute withput pdf
Hope you can figure out a way to merge them.