From Sorenson's support archives:

Workflow: Getting clicks and pops in my audio after encoding.

Operating System: PC/Macintosh
Product: Sorenson Squeeze
Version: 4.0, 4.1, 4.2, 4.3, 4.3.3

Issue:
I am hearing random clicks and pops throughout the movies that Squeeze
generates.

Cause:
We have now logged this as a bug. For now it seems to be happening when the source file has an audio track with 48Khz. It also happens if the source has audio of 16000 KHz or 32000 KHz. We are not sure of the exact cause yet, it seems like it has been made worse by some recent Windows or QuickTime update.

Solution:
The work around for now is to create a source file that has a 44Hhz frequency on the audio track. The other option is to convert the file to 44KHz in a program like QuickTime Pro before bringing the file into Squeeze.** However in the new 4.5 issue many people are seeing a pitch shift now when using this work around.