Why does the new version take so long to index the files I want shared. I have over 300 files that past versions just ate up but now it's been a few minutes and less then 100 files are in the shared files pane. I deleted all the preferece files and no change, am I the only one? Is it because of the HUGE support?

The indexing takes place only the first time you start phex, then the fingerprints are stored in file $PHEXHOME/sharedlibrary.xml. So if you delete this file, indexing has to be done again on next startup.