Since Domenica was not picking up an IP address and hence not responding to pings or ssh even after power cycling, I pulled it out from the IOO rack and connected it to a monitor. After a bunch of hit and trials, we figured out that the problem was related to the power adapter of the Rpi discussed here : http://www.raspberrypi.org/forums/viewtopic.php?f=28&t=39055
The power adapter has been swapped and this issue has been resolved. Domenica has been remounted on the IOO rack but left with the top lid off for the timebeing.
RF amplifier box:
The frequency counter was setup to read the beat frequency after amplification of the RFPD signals. The output as seen on the frequency counter screen as well as the epics values was intermittent. Also, locking the arms and changing the end laser frequencies did not change the frequency counter outputs. It looks like the RF amplifier is oscillating (Oscillating frequencies were ~107 MHz and 218 MHz) and the input circuit needs to be modified and the connections need better insulation.
As of now, I have connected the RFPD outputs to the frequency counter sans any amplification and we are able to get a readout of the beat frequency at > 40MHz (Frequency counter requires much higher amplitude signals for frequencies lower than that).