One thing that's not clear on that screen in the panel and in this thread is the context of the word 'username' as in
Specifically, the user name that is listed as USER in the web hosting column of "manage domains". If it says "Fully Hosted / user: johndoe" then that makes the path
/home/johndoe/mydomain.com/index.htm will be rendered to the user that visits
http ://mydomain.com (extra space typed to prevent the forum from hot-linking that.)
2nd thought: when you return to your browser and reload the page try pressing Ctrl-f5 (most browser) to force a server request, that should make sure it's not using something cached... If one ctrl-f5 is good then 2 are better
3rd thought: When you make changes in the panel, there is a delay before those changes are pushed out to the server. The screen often says the delay is about 10 minutes or something, I've found that sometime that estimate is low and it actually takes a little longer.
If you have changed the web directory, I'm not sure what you meant by "that's what I messed with a little bit ago", if you actually made a change via the panel that might be working against us.
BTW... watch capitization. index.htm and Index.htm are two different things (for example). Case is very import in file and directory names.