i always thought it was "atleast" but the spell checker shows me "at least".. but i guess i never learnt it as two separate words..

It's "at least". You can usually trust your spell checker. It's your grammar checker you need to be worried about.

The other one is definately. People are so sure their spell checker is wrong, they add "definately" to their dictionary. Well, the word is definitely. There's no "a".

Is there a reason why atleast is wrong?

Of course, there is a strong reason :"atleast" does not exist in the English language.