OK, I have compiled a test and simple code that proves the bug. I will share the files you can put on an SD card to replicate test:
test setup:
-Teensy 3.1 and audio shield, using amplifier line out left channel to amplifier then to speaker
-one copy of teensyduino 1.2 and arduino 1.06
-one copy of teensyduino 1.21 and arduino 1.61
-class 4 sandisk 4gb SD card (class 10 version made no difference for me)
-copy directory into root of SD card (large number files = 800 raw files)
-run playback interval set at 350ms (adjust volume variable as needed)
-faster you playback files, the worse the squeek/pop between files should get
-also different file numbers will have worse squeek/pop (how far into directory?)
-v1.06 should play a countdown verbally '1, 2, 3, 4'
-v1.61 should try to play same countdown, but skips many numbers randomly '1,3,4... 2,3,1, .. 3,4... 1,2,3...'
*I know bug got worse after version 1.61 arduino without my code changing at all. I can't play multi sounds at all anymore reliably!
*there is a 'squeek/pop' bug that I KNOW is somehow related to the number of files on SD card, it gets worse the lower you set playbackInterval
** if you try the same thing w/ only 4 files in the directory (one, two, three, four), the squeek bug goes away (may need to change file names on card).
Link to files (27mb rar file)
Please note, I had a similar bug with the old arduino wave shield regarding squeeks/pops with large file numbers. I ended up solving it by using play files by index (example in old WAVE_HC google code libarary). Basically you indexed file names into an array before starting the program, then playback files by the file number/address on card instead. This would be very valuable to us, and I imagine it could be as easy as playByIndex() or something in the audio library, and an index setup command.