I have a takamine EG523S and the oth day when playing ammped i noticed that the B and e (1st and 2nd) strings where the only ones making a clear and audable sound, the rest where not sounding(or they could have been very muffeld), the problem is with the guitar because my friend plugged his in exatly the same as mine with the same cables, equipment.. and it was fine.

Why is this?
Could it be a loose pickup? and if it is how do i fix this.
You are free to do what we tell you.
The EG523S has a split saddle right?

It could be that the saddle for the low four strings isn't seated down well enough
It could be that the transducer for the low four strings has come unplugged
It could be that there is a problem with the transducer it's self
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take it back to where you bought it and show them, dont let them put oil in your tail lights and make you believe its because your not using an acoustic amp or some ****E!