MSI H81M-E33 BIOS Issues and Post Flash Issues

Hello,
My situation is as follows: (TL:DR at bottom)
Built a new computer and decided to use the new LGA 1150 refreshed CPUs. Bought the MSI H81M-E33 Motherboard and installed windows. Noticed a problem with the rebooting even when installing windows. Thought it was just because of the windows installation, but problem persisted in which the computer seems to shut down but doesn't power down and i have to manually hold power button to power down and then push it again to start up. No real issues it seems since the computer does close processes and shut down but this was irritating me. I read online that BIOS updates seem to fix this problem. Did some research and decided to update with M-Flash to bios v6.6.
As I used M-flash to update to BIOS (selected "Select one file to update BIOS and ME") v6.6 the update stops at 47% and then the computer attempts to restart. BUT it still has the same problem and does not power down. So I manually powered down and started it back up. I then got "no signal" even as I waited. Now I'm freaking out and I power it down again and try again. This time I wait and it get to BIOS (MSI Screen) and then no signal again (not booting windows). Again I hold power down and power back on. Long wait again and I get back to bios. Still freaked out at this point but relieved I didn't brick motherboard.
Decide to flash v6.5 in case 6.6 was too new and might some problems. However v6.5 has the same problems; bios update stops at 47%, computer attempts to reboot, can't reboot, I power off, power on, no signal, power off, power on, wait a while and it gets to BIOS (MSI Screen), then boots to windows.
Right now the bios does read the bios version as v6.5 but I still have the issues in restarting where that doesn't really work. In addition, I now have this wait from pushing the power button to when I see BIOS (MSI Screen).
TL:DR
Had reboot problems decided to update BIOS
Used M-flash ("Select one file to update BIOS and ME") to update to v6.6
Update stopped at 47%, computer attempted to reboot, got no signal (reboot problem), powered off, powered on, waited a long time nothing, freaked out, powered off, powered on, waited a while got to bios (Whew), checked for new version (it is).
Decided v6.6 might be too new decided to try v6.5 used M-Flash again
Again stopped at 47%, computer attempted to reboot, got no signal (reboot problem), powered off, powered on, waited a long time, nothing, powered off powered on, waited a while got to bios, checked bios for new version (it is), save and exit, no signal, power off, power on, waited a while got to bios, then booted into windows
My concerns are;
I seem to still have reboot issue.
I have to wait for BIOS now, no longer pretty quick start.
My questions are;
Did I mess up the flashing somewhere?
Was stopping at 47% normal?
Should I try to update the BIOS another method to fix my current problems?
Am I missing a step somewhere?
Any help is appreciated, I just got really freaked out by the whole process but I'm just glad the computer still works (kinda).
Thanks in advance for any help, and apologies on the long essay just wanted to be as specific as possible.
-J
Specs:
MSI H81M-E33
Intel i5-4590
Corsair CX-430
Crucial Ballistix Sport 8GB
PNY Optima Series 240GB
Seagate Barracuda 1TB
LG 12x BD-Rom
Microsoft Wireless Desktop 2000

MFlash reboots in the process. To be sure reupdate using the below instructions and archive for a proper fpt flash. If you used Win8 feature (fastboot) before the first update be aware taht you need to set anything again after an update (e.g. enabling safeboot) as everything is set to default.
>>Use the MSI HQ Forum USB flasher<<
A.) Download the attached archive (E7817IMS_660.rar.rar) and place it on your desktop. Do not decompress.
B.) Download and install the Forum flash tool.
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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