Perhaps a PRAM Reset with the bare card should be tried.
Good suggestion, will try it later.
Anyway, the boot manager works well in 4,1 firmware with this card. Just stop working after upgrade to 5,1. Very strange, but at least we know that this card itself should have no conflict with the boot manager.
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Update 1
Your suggestion is correct. Do a PRAM reset with a bare card recover the boot manager.
However, I face another problem now. I tried to install bootcamp on my old HDD this afternoon. End up it doesn't wok well (Win 7 install OK, but then crash to blue screen during installing the bootcamp driver). So, I simply remove the bootcamp partition via bootcamp assistance.
And now, the boot manager works. But it only shows my old HDD (with 10.9.4 on it), and "Windows", but no SSD OSX and the recovery partition. When I choose Windows, it seems my Mac really want to go to the previous Windows partition, tell me "insert disk and press any key to continue" (the DOS boot fail screen).
When I remove the SSD, the boot manager doesn't shows the "Windows" option, but the recovery partition appear.
So, I am now confused. The Windows partition never install on my SSD, why it is now SSD related? Is it because I run bootcamp assistance when I boot with my SSD?
Anyway, a half working boot manager is better than no boot manager. May be do a clean install to the SSD can fix the problem.
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Update 2
After repair all disk in recovery partition. The boot manager die again. And can't be recovered by reset PRAM with bare card.
Back to the origin now. May be I should simply use rEFInd as a temporary solution.