I suggest you to watch MSI Forum Tool video incase you may missed something.
https://www.techpowerup.com/download/hp-usb-stick-formatting-tool/
https://rufus.akeo.ie/
Make sure your USB stick are on number 1 boot priority order. If it still not work then try put USB stick in every USB ports until you find a port that work.
If you still cant update BIOS 25.9 beta 3 with ME8 from bootable USB stick, I had time to read Z68A-GD65 (G3) user manual, you could try restore BIOS to defaults then enabled all USB 2.0 controllers, enabled legacy USB Support, enabled onboard USB 3.0 controller, disabled secure boot, disabled Multi BIOS Auto Update to stop secondary BIOS flash back to primary BIOS.
If above suggestion will not work then it worth a try to install Winki software from MSI DVD disc and then go back to UEFI setup to use Live Update to see if you can download and flash BIOS 25.9 beta 3, if it STILL not work then try disconnect SATA cable to your hard drive and see if USB stick will work in all USB ports.
So if everything failed then I had a great suggestion you to try flash BIOS from DVD and hard drive with bootable EFI Shell and forget about use USB stick because you cant boot the bloody USB stick in all ports.
1. Create new folder at root of C:.
2.
http://www.winiso.com/download.html to download and install free WinISO 5.3 version:
http://www.winiso.com/user/download/winiso-5.3.zip
3. The rEFInd Boot Manager
http://www.rodsbooks.com/refind/ to download CD image
http://sourceforge.net/projects/refind/files/0.11.2/refind-cd-0.11.2.zip/download and open zip file, move refind-cd-0.11.2.iso to new folder.
4.
https://www.wimsbios.com/amiflasher.jsp and download latest
AFUEFI Flasher 5.05.04 from AMI site
https://ami.com/?AMIBIOS_and_Aptio_AMI_Firmware_Update_Utility.zip and open zip with WinRAR, navigate to AMIFLASH/AMIBIOS/AFUDOS folder move AFUDOS.exe file to a new folder and also go to AMIFLASH/AptioV/AFU/AFUEFI/64, open AFUEFI64.zip and navigate to AFUEFI64 folder and move AFUEFIX64.EFI file to new folder.
5. Open BIOS 25.9 beta 3 file E7681IMS.rar and move both E7681IMS.P93 and valcheck.com files you downloaded from MSI forum to new folder.
6. Launch WinISO 5.3, navigate to new folder, open refind-cd-0.11.2.iso, move AFUDOS.exe, AFUEFIX64.EFI and to root of iso. Save iso and burn iso to DVD-RW disc.
7. Go to UEFI to boot DVD first priority, save setting and boot PC so you should see rEFInd Boot Manager and click on EFI Shell then look at device table for your DVD drive and try type in either AFUDOS and AFUEFIX64 command to flash BIOS 25.9 beta 3 file. If you cant find DVD drive on device table then you can try access your NTFS hard drive and navigate to new folder and try flash BIOS from NTFS hard drive.