Hummmm..... that is odd. Out of interest, how did you reindex the loops?
What I would say about reindexing is that the library doesn't just use exs instruments. It displays loops, instrument/ effect combinations using EXS24, Ultrabeat, GarageBand instruments, all kinds of stuff.
They way I reindex is to grab the folder with all of the loops in, so, Mactintosh HD> Library> Audio> Apple Loops> Apple and drag and drop it on to the loop library.
If you want to look at the library index for the EXS instruments then that is a different location and can be found at:
Mactintosh HD> Library> Application Support> Logic> EXS Factory Samples
and Sampler Instruments under the same location.
Hope that helps!