I can reproduce this bug on i386 and Kirkwood as well as on version 5 and 6:
TwonkyServer scans the whole directory (correct count of scanned music files) but fails to server them several times. I've checked the affected files via "mpck" and there are no errors in the files. It happens when browsing via Browser or PS3.
The log says nothing helpful: http://gist.github.com/raw/539964/89306 ... tfile1.txt