Figured it out. The D80 and D90 files/folders were missing from the CameraRaw folder, for some unexplained reason. I downloaded the latest DNG converter, which filled in the missing gaps.
Still don't understand how this happened, but oh well.
Was this with a Mac? Just asking because I was reading someone who lost their personal ICM print profiles on a recent Mavericks upgrade. The factory ones were still there, but their own ones they made were gone. Does seem odd as to why though.