idling rough and knocking

[sootnpretty]

so here is the deal, i just bought an 04 2500 CTD with 47k miles on it. yesterday after i filled her up i sterted up and i was kind of idling rough, so i drove it home and it felt fine. when i pulled into the driveway i noticed a knock, louder that it normally sounds and not a fast knock but i was definitely knocking but only in drive or reverse. so i shut it down and checked the oil and trans fluid, both ok. by now i was ****** so i let it cool off and me cool off went back out about 3 hours later and started it up and didnt hear anything. i drove it around and got it warm and sure enough once i came to a stop at a light it started idleing rough and knocking but only in drive and reverse not in neutral or park. so this morning i took it to the local dodge dealer and took them some TSB's that i had found. i talked to them later on in the day and they said that the were going to re-program the computer because there are four TSB on it all saying to re-program the PCM. now hopefully they will test drive it to see if the problem is fixed. does this sound right, who here has had their PCM re-programmed and it actually fix a problem, or the problem im having? i have been reading on the forum and im leaning to an injector problem, although it just started happening last night and there wasnt any sort of building up to the knock, it just happened. thanks in advance, im kinda worried because i have to pull my jeep up into the mountains this weekend for a wheeling competition thanks again, adam