1999 Tracker-Tail light issues

I have a '99 Tracker that i've had for 5 years. i went to get it inspected last week and the guy told me that it wasnt ready. he said that someone had unplugged my battery or hooked a code reader up too it. but as to my knowledge, no one has touched it. i had the issue of all my lights fading in and out, pulsating. But that is fixed (as of now). both my tag and inspection are both dead now and i am baffled as to what to do. the guy told me to have the chevrolet place "re-flash" my computer but i, as most, cannot afford the $100 to have it flashed as well as the inspection and tag dues... does anyone have any suggestions as to what i could do, or to what is wrong with my car?:banghead: