It took me a while to track the problem to something intrinsic to VLC. The Media Library will only remember 337 songs. I had at first thought it was because VLC was shutting down improperly (it crashed as I tired to use the Search Filter in the library). However, even after closing the program properly only 337 songs remain when it is launched again.
The way I am adding media to my library is going to the Add Directory... choice (after clicking the + button) and adding my ~/Music directory. This adds the files properly, all 12 GB and all 2120 files. There is barely a delay and there have been few playback issues (segfaults caused by bad files). However, as I said, closing VLC causes 1783 files to disappear from VLC's library. How many files can be added to the Media Library at one time?
Also, on a side note, the Search Filter seems to have broken between 0.9.9 and 0.9.9a, is this a known bug or also attributable to my large collection?
Thanks!
--Eric