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I have a 2 stage boot loader, the first stage loads the second stage and the second stage goes into protected mode, the problem is that the second stage makes my computer reboot :-/, any one know why is this?

perhaps if you gave a few more details... there are any number of reasons why your code could be causing reboots.

True.

Two of the thousands that came to my mind (I think the most important ones):

Have you verfied that your first stage works? (For example by printing out "Hello World" in realmode)
Are you sure your code is not triple faulting?