[jhandy]

honestly i dont think that it is a microswitch issue only becasue my window goes up and down regardless if the switchs are active or not.

IE: pull inside handle, window rolls up and down
outside the same.

Its not the regulator- because that is a mechanical device that either works crappy or not at all if broken. UNLESS you hear the motor working and window not rolling down.

I would look more to the motor. especially the connection at the motor and the wires that lead there.

Take the motor off of the regulator and see if it works up and down. if not then

unplug the motor. using a multimeter tool you should be able to see if the switch is working and sending a signal to the motor to roll the window down.

also look at the window button. May be broken. rare that both go out.
Also rare that both motors go out, or both microswitches, or both regulators, or both.... you get the point.

Look for something that affects both windows operations at once.

Also I dare say that It could be the ignition switch. That thing is known to mess up all sorts of electrical stuff that makes no sence at all.
For 12$, you can eleminate that as a choice.
Also weird that your alarm thinks that something is open. only becasue having something open will not affect the window operation. Unless your alarm brain got wet (under the seat) and has brain damage or something.