I've seen this, it was because of a very specific condition.
A DAT tape was recorded into protools. The clocking on the protools was on Internal instead of clocking to the digital input.
The original file looks perfect and sounds alright. (even though the record process was bad)
As soon as you process it with PnT, you see and hear exactly what you are describing.
We loaded the DAT and recorded into protools with the proper clocking. (sadly didn't think to phase match to the first recording). But the file then worked with PnT without any problems.
Maybe that info will help someone out somewhere down the road.

In Pro Tools 8.0.3 and 8.0.4, when using Pitch 'n Time Pro to process audio the resulting output is silence or "pops and clicks". This is due to an issue caused when using another AudioSuite plug-in to process the audio in the same session before using Pitch 'n Time Pro.

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Here are the practical solutions commonly used to fix Serato PnT Pro clicking issues:

Increase buffer size / latency
Go to your audio settings and raise the buffer size. Low buffers often cause clicks and pops.

Match sample rates
Make sure Serato, your audio interface, and your system are all set to the same sample rate (e.g., 44.1 kHz).

Update audio drivers & Serato
Install the latest version of Serato PnT Pro and update your sound card or audio interface drivers.

Use the correct audio interface
Avoid using low-quality built-in sound cards. A dedicated audio interface usually eliminates clicking issues.

Close background apps
Shut down CPU-heavy programs and disable unnecessary startup apps to reduce audio dropouts.

Check USB connections
Use a high-quality USB cable and plug directly into the computer (avoid hubs).

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I’ve encountered this issue before, and it was caused by a very specific condition. A DAT tape was recorded into Pro Tools, but the clocking in Pro Tools was set to Internal instead of syncing to the digital input. The original file itself looked fine and sounded okay, even though the recording process was flawed.

However, once you process it with PnT, the problems you described become clearly visible and audible. We reloaded the DAT and recorded it into Pro Tools with the correct clocking (though we didn’t think to phase match it to the first recording). After doing this, the file worked perfectly with PnT without any issues.

Hopefully, this information can help someone else encountering the same problem in the future.

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