A lot of times i can only make one of the throttle move at a time with my joystick. I tried to Push E then 1 then 2. But it doesnt work. What could be wrong. Is there another way to make fs select all throttles at once?

Go to the FS9 keyboard command list and get rid of the engine selector. When you accidently hit E key you select either engine one or two and never get them both back. In fact, I deleted all the default keycommands except for the ones I use. If you use a PMDG keycommand, you need the key free anyway.