Hello awesome people of UG. I've been using the site for a long time but never did use/or know about the forum. Hurray for google!

Anyway, this is my problem. I tune the the low E/6th string as close to perfection as I relatively can (which isn't much but not exactly bad). I then proceed to the A/5th string. Then to the D/4th string and so on till I feel proud of my little accomplishment. Then upon checking the whole thing something sounds off. I repeat the process starting with low E but still the sound persists. I use a digital tuner and prepare to repeat the whole thing again when I notice that the 5th knob affects the 6th string. As does every other knob on every other string. My mind exploded and its near 2 in the morning and googling shows the other problems similar to mine were one from 2007 and mostly about tuning E to drop D producing minor changes. Mine are a little more than minor though. A full tune of everything would result in the 6th string going D or even B. Yeah that bad.

Oh and a few more things. My strings are new. I've shifted from 9s to 10s. This guitar hasn't been used in about 3 months. Please help. Thanks!
try tuning 6th string, 1st string, 5th string, 2nd string, 4th string and finally third string