Z87-GD65 now booting very slowly

Hello,
Last week I booted my PC and found it didn't boot to Windows in it's usual ~6 seconds.
Instead it gave me a black screen for about 3-4 mins before eventually the boot screen displayed and then the Windows login page.
After looking at the debug codes on the motherboard I saw it did this:
first it stayed on the code "9A" for about 40seconds, then it changed to "A2" for about 2-3 mins (at which point the black screen displayed A2 in the bottom right corner). Then after this it then booted as "normal".
I've tried unplugging all extra hard drives (excluding the OS), and also I tried to booting to a different hard drive with the Ubuntu OS installed - but this gave me exactly the same sequence of events. I also tried plugging the SATA cable into different sockets on the motherboard.
Maybe I should add that the machine is about 18 months old, it had the latest BIOS installed... That's all the info I can think of right now.
I'm not particularly experienced with this, so if anyone has any advice or ideas of things I can try I'd appreciate it a lot.
Many thanks !

Properly reflash bios A with latest bios including ME firmware update:
A.) Download >>this archive<< (E7845IMS_1B0.rar) and place it on your desktop. Do not decompress.
B.) Download and install >>the MSI HQ Forum USB flasher<<.
C.) Insert your FAT32 formatted usb stick.
D.) Make sure that all win 8 options are disabled. (Fast Boot etc) Also make sure the legacy USB is enabled.
E.) Start the forum flash tool and select option 1. Then point the tool at the compressed archive we downloaded earlier. Then to your USB Flash Drive.
F.) Boot to the USB 
G.) Now follow the directions and let the tool flash
H.) After flashing reinstall ME drivers in Windows:  http://download.msi.com/dvr_exe/intel_amt90_mb.zip

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