USB Keyboard Cuts out During startup

OK so I have a Dell Optiplex 780. Onboard NIC went so I had Dell send out a new motherboard, and I replaced it this morning. Swapped everything out, turned it on, and I must have not shut down windows properly when I brought the computer back to my workstation. The issue I am having is when windows loads that screen that gives you the two options "repair windows (recommended)" or "start windows normally" the keyboard and mouse cut off. After 30 seconds it defaults the repair options since I cannot pick start windows normally. Once this loads I regain keyboard and mouse functionality. Repair cannot find anything wrong, yet it will not go past this start up screen letting me know windows was not shut down safely. All I need to do is tell this POS that windows was shut down correctly via the command prompt, or get the keyboard to not cut out. So far I have tried a different keyboard (only USB keyboards, no PS2 port), reset the cmos, ran the Dell Diagnostics (no errors were found), and cursing Dell. Does anyone have any idea to get around this? Windows is not corrupt, I just need it to start normally.
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  1. I have also tried different USB ports. I can hit F8 to get into safe mode, but once that menu pops up the keyboard again goes out.
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