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Stereo Tool operates in bursts so if your CPU isn't very fast it will - for every 42 ms of audio (at default settings) - take a while.
The CPU is a Intel Core i5-3330 at 3GHz and with version 7.60, which have a much higher CPU utilization, the problem it's not present.
The sound card is an ESI Juli@.
Clicks seems randomic, not periodic.
I would guess it's related to the CPU load at the moment a new burst ends/starts.
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Does lowering the Latency in ST help as well?
Yes but it's different for 7.70 and 7.72.
In 7.70, lowering to 1024 mitigates the problem and even better at 512 samples the problem it's rare but still present.
It's really weird at 2048 samples, in the right channel sound is completely distorted...
In 7.72 things goes better even using 1024 samples but 2048 still result in distorted sound on the right channel.
I've also noted another thing... clicks are present randomly at left or right channel.