IMO this issue becomes quite serious these days!
I got a brand new Samsung Galaxy S3 and since it has "only" 16GB of internal RAM I always store my media (music, videos etc) on my external SD-card (32GB).
Nowadays this card is mounted in /mnt/exSdCard (not on /mnt/sdcard/externalSD) !
Twonky Mobile though insists on searching for media on /mnt/sdcard (it seems to be hard coded since every change to the relevant XML or INI files won't persist) hence TM won't find my media.
Since this new mounting points seem to be the new default within Android ICS it TM will never show any media content stored on external SD cards anymore.
This is a BUG! Please fix the standard search directory at least to /mnt