tranny doesnt know what gear to be in HELP

[08kingranch6.4]

so i was running the spartan 310 tune and never beat on m truck until a little civic pulls upto me revving his engine.. had to put it on 4hi and boost it a lil bit. blew his doors off. next stop light i go to start and it felt like a was starting in 3rd or 4th! i tried shutting it off and putting it into neutral and then it started in first again only problem was it wouldnt shift out of first! so as i was doin about 25 in first i put it in neutral really quick then back in gear. it stayed in neutral! has any one seen or heard of this. help please!