MPower Z87 - strange bahavioure with SSD - Unable to upgrade BIOS

My Spec:
CPU: i7-4770
Mobo: MSI Z87 MPower (MS-7881) 1.0
Chipset: Haswell Rev.06
Bios: v. 1.3
Memory: G.Skill 2x4GB XMP1.2 Dual channel
Graphics card: GeForce GTX 660
PSU: Seasonic M12II-620Bronze - 620W
HDD:
WDC WD20EARS-00MVWB0 - ATA8-ACS-SATA II
WDC WD20EARX-00PASB0 - ATA8-ACS-SATA III (MSI tested - ok)
WDC WD20EARX-00PASB0 - ATA8-ACS-SATA III (MSI tested - ok)
SSD:
Samsung SSD 840 (256GB) - ACS2-SATA III
Toshiba THNSNS128MCP (128GB) - ATA8-ACS-SATA III
*According to this: http://www.msi.com/file/test_report/TR3_2851.pdf
PC - Windows 8 x64bit
Laptop - Windows 8 x64bit
Strange thing happens yesterday, I did run above setup for over a month now without any issue (excluding HDD A2 detection that took around 30sec-45sec). I did copied some video files (3files - around 2GB) from WDC WD20EARX to my Laptop over network (SMB - or whatever proto. Windows 8 x64 uses these days) and copying just stopped - no error or anything - just progress stopped. So I tried to kill Explorer process - without success. On my laptop I couldn't access these directories with the error "Unable to access...". So what I did was to restart PC - not hard restart but windows Restart. I did same on the Laptop. Laptop boot up properly but my PC did not.
   On PC during boot I can see 99 -> 9C -> A2. At first 9C was fast, after some reboots it's taking now 30sec+, and A2 ... takes 10minutes. Strange part is that after that time everything is working fine. After Windows 8 turns on I did scan drives and non of them had an error.
   And now it's a kicker - I did copied all my data from mSATA drive (Toshiba one) and removed partition and reformatted drive - PC now starts after A2 like - 30 sec.
   But still booting up takes like 9C (sometimes its faster) - 30sec, A2 - 30sec -> 10min.
   Also I did tried to update BIOS from 1.3 to 1.5 or 1.4. After selection in BIOS file motherboard just freezes.
So questions:
1. How long it takes on MPower Z87 to detect drives for You guys? (on my 9C - 15-30sec, A2 - 15-30sec - total boot detection time is around 1min)
2. Why I cant update BIOS?
Thanks for reply
Regards

I almost brick my mobo. I did got my USB drive prepared and after reboot on "Do You want to run Mtest before update" I did press Y, although instead of running Memtest it went back to my boot chain - so boot into OS, and halfway during boot power was turned of...
Now after disabling setting up 1 drive for boot device (was that before update) I can see that speed increased.
EDIT:
Ok it did not helped at all, now its even longer to boot.
What's strange is that after 1st boot after BIOS update everything went OK == fast, then after reboot from Windows slowness starts again. No changes to BIOS settings...
I had exactly same situation with WD EARS, repartitioning helps but if this occurs again on that drive then I'm in big trouble as I don't have any more 3,5' USB HDD bay.

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