No USB or SATA on G31M3-F intermittently

I have an MSI G31M3-F motherboard and it seems whenever I do some kind of hardware swap, for example add a hard drive, when I start it up, it doesn't recognize my USB ports or SATA ports.  Even if I revert the computer back to the exact setup it was at before doing the hardware swap, it still won't boot with USB and SATA.  If I leave it off for a while though, and turn it back on (like the next morning), everything's fine.  And then I can turn off the computer and back on indefinitely it seems, until I open the case and mess with hardware.  I updated the BIOS to 1.3 (the latest) and that didn't seem to help.  Do you think the board's just bad?  Thanks for your help

OK, here are some more details about my system:
# Intel Core 2 Duo e7200 Wolfdale 2.53 GHz
# G31M3-F motherboard with version 1.3 bios
# 2 1 GB memory sticks, Kingston KVR800D2K2
# Video card: GIGABYTE GV-NX86T256H GeForce 8600 GT 256MB 128-bit GDDR3 PCI Express x16
# Seagate 500 GB SATA Hard Drive
# No other add-on cards - peripherals: USB keyboard and mouse, USB printer, speakers, monitor connected with VGA cable (DVI to VGA adapater)
# OS probably not relevant since problem is at post, but it's Windows XP SP3
# Antec 430 W power supply, +12V1 17A, +12V2 17A, +5V 2A, +3.3V 28A
Another note: The system was just working fine at the above configuration.  Then, all I did was turn off the system, open it up, and connect an additional SATA HD (Deskstar 1 TB) (power and SATA connection of course).  Then when I powered up the system, I had no USB or SATA ports, so the system wouldn't boot.  When I went in to BIOS, it did not detect either SATA drive, and I couldn't get into BIOS with my USB keyboard, I had to use a PS/2 keyboard.
Thanks!

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