I have had my 01 Bugeye since May last year. I am now having the same problem for the third time.
When I picked to car up it was fitted with a very good Clifford, but the one key would not start the car. So, the Subaru Dealer changed the key.

Still had the fault.

They then fitted the standard Sigma alarm back on saying the Clifford must be at fault.

Worked OK until before Xmas.

Faulted returned with the same key. I rotate them for wear etc.
Re-programmed, came out of the garage, still on the forecourt and the same happened again.

Another new key fitted.

Fault is now back, same key??????

It's always the new re-programmed key??
FAULT
Get in stick the key in, car turns over, does not fire and the key symbol appears on the dash. Sometimes after a few goes it starts, sometimes only the other key works.

HELP!!!!!

 

The problem here is related to the factory transponder immobiliser and/or the chip within the key housing itself.
If the problem was due to the alarm the engine would not even crank over.
The fact that key symbol appears in the instrument cluster also backs this up as it also relates to the factory transponder immobiliser.
As the problem keeps recurring, despite new keys, I would ask the dealer to look at the transponder loop around the ignition barrel itself, connections to this and the engine ECU as a last resort.
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Ta!!!