Dear everyone,
Thanks for all your inputs.
I was able to get my hands on an Isolated DSO, and was able to probe Vgk, Vo and Vin simultaneously. As FvM pointed out, the SCR was not getting triggered because the pulses were not being generated.
Upon further investigation, it was found that the 5mH/25A inductor was the only problem causing element in the system as it worked in case only a C filter was used.
The input to the SCR is via a 230V/120V 2.8kVA transformer, and the firing was generated after tapping the secondary for ZCD reference. This problem of pulse skipping was solved after taking the reference from the primary instead. The LC filter was maintained for the same and thus we didn't have problem in retaining the L for filtration purposes.
Any clues on why it happened? Was it EMI that was getting reflected on to the control side causing this havoc? Thanks.