Mmm.......this really feels like over-aggressive power management (power saving) somewhere - have you been through the bios settings ?
Tony
Lets find out if its network related, firstly can you go to your network adapter and disable IPV6, does anything change on a test.
If not then I would be tempted to change any reference ip within TVServer\MPClient\SQL to the name of the pc, again this will need services to be restarted, user for sql db can be sa or root, with password MediaPortal case sensitive.
Any difference.
Last resort, try the MSLoopback adapter, which should eliminate any possible networking problem, if it does then going down the fixed IP road may be the solution.
Even with Windows Firewall disabled, it can still be active so I'm wondering if starting MP on that machine allows ports to be opened properly, btw what router do you have.
http://www.homenethelp.com/web/howto/static-ip-address.asp
The only other thing that mediaportal.exe does is start directx and ups using the graphics processor you have, really cannot think of any other effect caused by MP starting ;(
2 other possibilities have come to mind, try disabling any defragment when idle setting (if enabled of course), and maybe switch off pagefile (reboot required).
Yes, you also went for the obvious hardware settings, so thanks for reporting back on that, last thing I can think of, is HDD going into some kind of slowdown thinking its idle, I have read this in the past regarding WD drives, where a drive bios update was required, might be worthwhile googling the model, just to see if any reported problems there.
After that I'm really baffled