Thanks for the suggestions. The number of possible reasons were many and the lengthy boot time made it very tedious. Here's the final fix and how I finally found it.
After updating the BIOS of the desktop, I saw a message during boot that the AHCI BIOS wasn't installed. Since this system didn't have SATA drives I searched for another reason. The search suggested disconnecting all USB devices. I disconnected all except the mouse and keyboard.
The system booted right up, but the mouse was erratic. I stopped using that port and hooked up all the other USB devices, both directly connected and through a USB hub. There has been no problems since.
The troubleshooting was complicated because it started right after the software upgrade.