Actually, there is a fix!
This issue plagued me for a full year. If you read my previous note it will help you understand the problem. It has to do with the actual .plist file: ~/Library/Mail/V2/MailData/Accounts.plist
Multiple email accounts in Mail.app, causes the issue to appear. The order in which the accounts appear in this file causes the problem. In my case, I couldn't keep any of my sent from one account until I finally manually edited the .plist file. I sent logs upon logs to Apple trying to help them find the problem. They finally closed the case without a solution.
I have since verified that in most cases, you can manually drag folders around in the folder area and fix the problem. In my case, I had to fix the plist file with an editor.
To fix the problem using the folder area: Make sure that the mail server you're not getting sent from is at top of each section. Meaning if you have two servers: Mail1 and Mail2, and sent is being lost for mail2, move mail2 to the top of each section (i.e. Inbox, Sent, and location of the servers in the folder list). If this doesn't work for you, you might have to edit your plist file like I did. If so, read my previous post.
I've had this Bug Report in on this for over a year, and I finally fixed it myself. When I told them I fixed it, they finally asked for the fix, and I sent them the details, hopefully the next release they their bug and repair these issue automatically.