At the bottom of the page there is a utility called fifofo.exe. If you run this it will check your fonts folder and list any errors.
High-Logic produce a Truetype Font Editor.
Possibly, during the copying some fonts were not properly registered. Over 1000 fonts is a lot, but I think that XP can cope with that many. I keep most of my fonts in another folder, and install only the ones I use regularly. If I find I am missing one, it doesn't take long to install it. Just over 500 now which is too much for ME.