Got it working.
This is the combination that would get it working again.Here's "fix" .
Plug in Flicr to USB port and wait for the app to show "connected"
Now go to clear config.
Once done remove Flirc
Plug it back in and start recording keys - this time its recognising key presses.
NOTE: when i tried clear config and then configure keys without disconnecting it that did not recognise key presses.
I dont know if this fix will be good now for long term or will it soon forget settings again. I'll keep you updated.