After huge lighting storm, motherboard doesn't power up USB on startup

It used to work no issues at all until a storm hit a few days ago and caused power surges. At first I had issues even booting up my computer, it would get stuck forever at the Windows energy logo during the bootup process for Windows 7.

Now I having USB issues. This seems to be OS independent and happens on the hardware/BIOS level. I have an external Seagate USB 3.0 harddrive (flat/thin) that connects directly to one of the usb ports on the motherboard (Gigabyte Z97). This external usb drive gets its power from the usb itself and does not have a separate power source. I also have a brand new 750 Watt PSU, and only one graphics card and nothing else that consumes power.

Whenever I reset my computer, I notice the light indicator on my external usb does not come back on, and even when Windows 7 loads, it does not pick up the usb drive. However if I unplug and plug it back (regardless of whether from the usb port side or the other side) it immediately shows up and is usable without any further issues. But the next time I reset my computer, it doesn’t see it anymore.

The only way I can get it to see it and to power up itself on restart is if I hit the switch on my PSU to turn off power completely, turn the switch to ON on the PSU, and then power up my computer from a cold dark reboot. Then I heard a lot of whirring noises and it seems a lot of juice is being sucked up and everything is powering on, and it is only in this cold start that I see my external usb drive light comes back on, and then when Windows loads it picks up and recognizes the drive without issue.

However if I soft reset the machine, or power down the machine without power cycling the PSU, the next time I boot up the sound is noticeably MUCH quieter, and also the light on the external USB does NOT come back on. However, I can immediately unplug and plug the usb drive back into the same usb port and it will come back on… But if I do a warm boot or soft reset it never seems to pick it up itself without me having to unplug it and plug it back in.

How can I set the BIOS or whatever to get this to work without having to power cycle the PSU or unplug and re-plug the external usb cable each and every time I reboot or shutdown and start the PC back up?

Is there a way to force the motherboard to shutdown for good, so that when I power it back up it does the cold boot each and every time?

I also have a brand new 750 Watt PSU

Brand new before, or after the lightning storm? You need to verify your PSU did not take a hit and that it is still working properly. Easiest way to do that is swap PSUs with another known good PSU, or take your PSU to a shop and have it professionally tested. You don't want to keep trying to boot this one if it keeps failing as that may be causing more and more data corruption.

In the end, you need to consider putting all your computers and expensive electronics (big screen TV, home theater) on "good" UPSs with AVR (automatic voltage regulation) to help protect your equipment during bad power times.