Looks like CPU tuner cannot identify VoIP calls (which I do using Sipdroid) as a call in progress.
When Sipdroid turns off the screen during the call (due to the proximity sensor being activated), CPU tuner triggers the screen-off profile instead. When this profile is configured to reduce the CPU frequency, this leads to codec/audio stuttering and dropped calls.
Anonymous
PS: Using version 3.2.1 on a Motorola Flipout with Android 2.1-update1.