My guess would be that it's nothing serious and just related to the VIN & title dates not matching. I would cover my bases, though, and find out best & worst case scenarios before I went in, just to be prepared no matter what they say. I'd guess that, worst case, you might lose the current title and have to wade through some paperwork to get a new one that includes all of the info related to the truck (specifically why numbers may not match from body to frame). I don't think, unless something comes back as stolen, they can do anything to you personally.
I had a similar experience when I went to re-register my '75 in Ks back in the early 90's. The EB that I had originally titled & registered was totalled so I didn't maintain the registration. Once I got it all rebuilt (another '75 frame and a '66 tub), I had to take it in for inspection so I could re-register it. The Trooper on duty asked me tons of questions and started giving me a hard time about the bill of sale I had for the tub. I likely should've just told him that everything lapsed because I was away at college and restoring it, but I stupidly told him the truth. To this day I think the only reason that I was able to get it out of there without issue was because a good female friend from highschool worked at the trooper station and, apparently, appealed to the trooper on my behalf.
Good Luck!