AHA!!! Yes, I normally tune down to D also for the same reasons you do and after updating to HD have the same problem with "clashing tones" on the 12 string electrics, haven't trie the 12 string acoustics as I only had a few minutes to play the guitar the day the update was announced. I believe it was the D string going haywire on my guitar also, tho I also have a bunch of crazy noise on the E that wasn't there before and is likely caused by slight fret buzz. I have not tried tuning up to E to see if this corrects the problems, will try first chance I get BUT I still want to play tuned to D as I prefer the string tension in this tuning - if the problem is fixed when tuned to E I am going to report this as a bug.
I mean other than the anomaly with tuning the D string down to C... The other strings don't clash? I don't tune my guitar down but have thought about dropping it down a half step and using virtual capo to bring it into 440 but haven't tried it yet.... I guess I was questioning on a purely selfish reason and not to figure out your own issue... And for that I'm sorry.
Update: I notice that it DOES affect 6 string models and sitar when using alternate tunings or virtual capo's when the "D" string is tuned down a whole step. Without the alternate tunings or virtual capo's on the 6 strings, I didn't hear the "D" string clash. I didn't test every model or scenario.
Jeff: Correct, the other strings don't clash (that I've noticed) when tuned down a whole step, just peculiar to the "D" string. This clash is a MAJOR glitch in my opinion, so my initial request is to verify whether it is just my guitar or a common issue.