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We suggest you implement the fourth specification change stated on page 38 of the Intel Atom(R) Processor E3800 Specification Update document # 329901.
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Our PMIC controller does indeed sequence V1P8A before V1P0A. This is as specified (note 5 table 61) of the family datasheet and we have always used this sequencing. Our PMIC controller is BD9596MWV-M from Rohm and this is their preferred sequence.
Unfortunately we are in a mature design phase with product release later this year, we are currently going through EMC compliance testing. Given this sequencing is not "recommended for new designs" is there a recommend work around for old designs? Is my current work around of manipulating the PMC_PWRBTN signal adequate for production? This work around is fixing all effected units but I'm reluctant to commit to this until I'm aware of the root cause of the issue, we can't have units failing in the field due to this problem.