"I don't think the Pro In-App Purchase is working correctly"

The "Purchase Upgrade" dialog is designed for exactly that -- to purchase upgrades from the App Store. Some early users got themselves into strange situations, so before allowing you to make a purchase, Composer requires you to Restore Purchases first. This is to ensure that you do not try to purchase something you already have. (Presumably the App Store prevents you from doing this, but I can't control the App Store and have learned that Apple still needs to iron out some bugs in the handling of In-App Purchases.... so extra precaution seems wise).

The easiest way to verify that you have Pro Functionality is to check and see if the Pro Preference pane is present in the Preferences dialog. The easiest way to verify Standard functionality is to open more than one file at a time.

If you are truly having trouble with In-App Purchases, you can send me the receipt file from inside the application bundle and I can verify it on my computer. It is located here (assuming you have Composer in the /Applications folder):

/Applications/MultiMarkdown Composer.app/Contents/_MASReceipt/receipt

Sending me the receipt can help validate whether Apple is giving you "credit" for in-app purchases or not. Theoretically, there could be a bug in my receipt parsing/validation code that could lead to Composer ignoring a prior purchase. As of yet, this has not happened, but it is possible.

That said, I am limited in what I can do to fix problems. Apple does not give developers any "special access" into your account -- I can see my account and that's it. So my recommendations in general are:

1. Verify that you are using the proper iTunes/App Store account. Purchases are only available from the account used to make the purchase. If you have multiple accounts, this may be the problem. Switch to the proper account and download the app again.

2. Use the "Restore" button in the "Purchase Upgrade" dialog to ensure that you have the latest copy of the receipt. Relaunch the app and check for the Pro preferences again.

3. If that doesn't work, delete Composer and download it again from the App Store. Check preferences again. (This has worked for several people who had trouble.)

4. If it's still not working, you can send me the receipt so that I can verify that the problem is with Apple and not Composer. This could at least give you some "extra ammunition" when contacting Apple's support. Unfortunately, there is nothing I can do to troubleshoot things on Apple's side, so you will have to reach out to Apple for them to look into what is going on. If this happens, I would still appreciate an email just so I can have a sense of how often this sort of trouble happens. (Thus far, I believe only one person has truly had trouble to the point where they had to deal with Apple, and that was when redeeming a code for a purchase, not restoring a previously made purchase.)

I hope this helps, and definitely let me know if you're having trouble that this doesn't solve!