You're only seeing "1" control because you're searching te Master Page, not its Content.
To find a control on a page that has a master, you have to do something more like this:
this.Master.FindControl("MainContentPlaceHolder").FindControl("MyControl")
Adjusting the IDs as necessary, of course.
Controls also have a unique ClientID that looks like this:
ctl00_MainContentPlaceHolder_MyControl
Do a View Source in your browser to see what your controls are actually being named at runtime. You
could do a FindControl using that ClientID, but it's cleaner to do it the first way.