If you want to do this without starting Steam and logging in, you can modify the setting in the Windows registry. The autostart checkbox is directly tied to a registry key — simply deleting it is all the Steam client does when said checkbox is unchecked.
Navigate to HKCU\Software\Microsoft\Windows\CurrentVersion\Run and delete the Steam key. Or as a .reg file:
Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run]
"Steam"=-
I know of only one way that this can happen in windows, and has nothing to do with Steam other than their not-so-great decision to install all content into Program Files.
If you are on Windows 7 or Windows Vista, and you have UAC set to ON, then change it later to OFF, this can happen.
UAC does thing evil thing where if a program tries to write to a "protected" area like Program Files, EVEN IF YOU ARE ADMINISTRATOR, when you get a UAC prompt and give permission, it actually writes any files that would normally go into that directory into a "virtualized" directory somewhere else.
If you turn off UAC, that will no longer happen, and as an awesome bonus, it will no longer know about the files that it virtualized.
So in your case, if you had UAC on, installed a ton of games, then later got sick of UAC and turned it off, this would happen as you described.
See the second paragraph in "Features" in the article on User Account Control.
If you have done this and turn on UAC again, your content will come back, but be a TOTAL mess because if you've downloaded more stuff with UAC off, then that will be invisible when you turn UAC on, and vice versa.
this drove me a little crazy once before I realized what was happening.
i'm curious to know if this is your issue.
Best Answer
I've had this happen to me. After you patch, Dota sometimes fails to recognize that you have the most up-to-date patch. It's frustrating because you don't get an error message that would lead you to this. However, it can be solved.
Simply log out of your game, go to your steam library and right click Dota 2. Select Preferences, and find "Revalidate Game Cache", this will force your game to re-update, and should solve your problem.