I tried it out today using the default microphone inside my laptop and it said my low E string which is slightly out of tune is a B, then an A#, which cant be right.

Does the tuner even work properly?
It works properly for me. Did you compare it with a real, external tuner?

ps: I put my guitar through line-in
Yup I just used my laptop microphone and it couldnt pick it up properly, I guess you need to plug the guitar in or plug in an external mic and put the guitar close to it