This is a phrase largely equivilent to fucked up or screwed up. It roughly means "in a state of disarray" and is commonly used in the phrase "to jack someone/something up". In some cases, the meaning may be slightly altered by the fact that to get "jacked" can mean to be struck or injured.
That's jacked up man. I can't belive your girlfriend is cheating on you.
I got in a wreck last night. My car got totally jacked up.