A few days ago, I posted a note about having problems with a Mac Pro, a Huge Systems FC array and the Kona LHe card. The problem is fixed and it turns out it had nothing to do with the Kona card.
While waiting for ATTO to release new drivers for their FC cards, I'm using the Apple FC card. It's a 2 Gbps card and the array is 4 Gbps. The problem was caused by the Huge array not setting the correct link speed. It's supposed to work just fine with a 2 Gbps card but it was usually dropping all the way down to 1 Gbps. That explained the 90 MB/s performance, instead of the correct 170 MB/s. At the suggestion of Huge tech support, I upgraded the firmware of the array and the problem went away: every time the Mac boots, the array is now correctly connecting at 2 Gbps. Huge tech support suggested I could manually force the array into 2 Gbps mode but after the new firmware was installed it wasn't required.
I had thought the problem was Kona-related because during several tests, taking the Kona card out gave me the correct performance on the array. However, it turns out this was just coincidence: it was turning everything off to remove the Kona card, not actually taking the card out, that made the difference. AJA is actually sending me a new card anyway, which might not be a bad thing anway (perhaps there is newer firmware in the card; I don't know).