I have done a couple quick tests to see if the posted issues can be reproduced.

Reboot - survived (w/ overclocking settings saved as default)
After phone call - nothing happened
Conky - yes it's running the xlv profile at 1000/1000

My device: PR1.3, swappolube proposed settings, overclocking@1000min/1000max

How I flashed:
The machine first got a clean install with PR1.3 and the original eMMC image,
then exchanged the 2GB ext3 partition and the 27GB vfat partition,
then installed and ran swappolube with the proposed values
finally installed the power kernel (v3.7 from extra-testing repo), used xlv profile then manually edited it to set both max and min frequencies to 1000, and to avoid all the allowed frequencies except two following to jackiman's instructions