apps missing from My Apps part of Market
Do you have multiple Gmail or Google apps on your domain logins? I found it confusing, because whatever email account I happened to be reading became the current account in the Market.

So some of my apps ended up being assigned to these other accounts until I figured out that I wasn't logged in as expected. I didn't realize it because they were free apps so there wasn't the issue of requiring a registered credit card for these other logins.