How to change pin mode in BBB?

I want to use nearly all pins on my BBB in GPIO mode, and for that I have to change their mode according to several tutorials. For that I have to execute a command into omap_mux. But this command does not work for a kernel > 3.8. Therefore I used this tutorial:, and I wanted to use GPIO86 aka lcd_vsync. But regardless of my inputs this output always stays at low with several sharp peaks (I assume these as the sync signals). What am I doing wrong? What do I have to do for using it?
On other pins (for example GPIO60) that works, so I think that the problem is the current pin mode.