Your problem happened to me one time. When I selected My Apps it only showed 2 apps but my application drawer still showed the correct amount of apps (about 200).
While you are on the Market, click the Menu button, then click on Accounts and make sure that the correct account is selected. For whatever reason, my yahoo account was selected instead of my gmail account. Once I made sure that my gmail account was selected, all of my downloaded applications showed up when I clicked on My Apps