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Hi,
Are you able to solve your intermittent issue? Also using Arria II device.
I have similar intermittent ltssm issue during power-on.
Regards
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Mine was an issue caused by the Reset controller in the Reference design. The reset controller has a statemachine which is asynchrnously reset by a signal fed directly from PLL's lock --> The statemachine goes to unknown state sometimes and the HIP can't be initialized properly.
Exactly where I can't recall. Please trace it first if you still can't find it, I may need to dig up the code.
Remember, reset controller, PLL's lock signal --> Resolved by a simple synchronization of Reset to the clock domain.