Same here, no resolution after 6.0.1 update. I don't even think this is on Apple's radar. Apple "geniuses" don't care about this issue...I've asked. Here are my steps to re-creating the problem:
1. Reboot the phone normally (just to get a "fresh" start).
2. Turn up the phone's ringer volume and notice the volume of alerts and keyboard clicks.
3. Activate Siri and ask for the weather.
4. Double click the home button, swipe right twice to get to the audio volume slider.
5. Put the audio (iPod) volume slider in the middle.
6. Notice the volume of alerts and keyboard clicks.
7. Double click the home button, swipe right twice to get to the audio volume slider.
8. Put the audio (iPod) volume slider on the far right (max volume).
9. Notice the volume of alerts and keyboard clicks -- they should be barely noticable now.
** 10. Reboot the phone to get the alert volume working normally again...don't use Siri unless you HAVE to.
This is really irritating as I SOMETIMES use Siri when I'm getting ready for work and I want to know the temperature outside without having to stop what I'm doing. Then my alert volume is messed up until I reboot.