Weird Shortcut Duplication Problem

Some unknown program or software malfunction has caused the duplication of large numbers of shortcuts on one of my PCs. Naturally, it is the older PC with Vista Ultimate installed. (When I built a new and better PC, I installed XP-Pro again.) The installation is not new, but the shortcut issue is. I don't know what caused this; nor exactly when. The desktop shortcuts are not duplicated, and those are the ones I most often use, of course. Today I had occasion to go into the start menu and found applications and files with as many as 20 or more duplicates or as few as one. A search of the C-Drive turns up in excess of 2,000 shortcuts; most of which are in the "ProgramData" Folder. Most of those are duplications. I deleted a few hundred manually already and am currently running a fresh search. (Files deleted from search sometimes are not deleted from view until search is closed and re-started.) I considered using "Select All" and deleting all shortcuts, but I would prefer not having to re-create single shortcuts for more than 130 programs, plus sub-applications, files and folders. I tried my duplicate files manager, but it isn't really more usefull than the search function.I need some way to eliminate just the duplicate shortcuts, all of which have numbered parentheses suffixes. Isn't there an easier way to do this than sitting here for hours and manually selecting and deleting. And How do I insure no repeats? Does anyone have any suggestions? It is a weird situation.

System: Pentium 4, 3.2 GHz, with 2 GB RAM
OS: Vista Ultimate, Build 6001 with SP1. (Problem occurred after SP1 install, almost cetainly not as result of SP1)