Please take a look at latest cgminer driver. The PLL code was re-written to match updated specs quite some time ago and was merged upstream just recently. The issue was a misinterpretation of the PLL formula that got clarified with the latest chip documentation. It affected system clocks below 250MHz, so exactly your case. Please let me know if the problem remains.
As for the chip temps: as soon as the chip starts hashing, it instantly gets very hot. At nominal 800MHz, if you have no top heatsink installed, it reaches almost immediately 60°C with proper back heatsinks and more than that without. Obviously this also highly depends on the supply voltage, which is supposed to be on a safe side over 820mV. This requirement is unfortunately chip specific, so you might find some boards going just fine with 760mV while other are more picky with chips resetting immediately below 820mV.
As for the HW reset: this is always board specific. As reference, please check the A1 board selector sources where reset is performed with different types of i2c board expanders.
Zefir, thank you for the quick reply. I am going through the code right now. I just wanted to quickly confirm something with you - the integrated code is specific to the CoinCraft Desk and communicates over libusb (rather than RPi SPI headers), correct? Thus, I will be merging some of the new stuff (such as the updated PLL code) into the old RPi A1 driver code?