Sounds to me like the registry is getting change back to default at reboot. Here is a link to
SpeedGuide and on this page you will find the registry setting for MTU.
Quote from SpeedGuide:
Customizing the Windows Registry assumes some proficiency in tuning Windows configuration files. If you don't feel comfortable editing it, please use our TCP Optimizer program, or the Windows 2000/XP registry patches from the Downloads section of the site. both those options will add all the parameters and set all the optimal values in the Registry automatically for you.
I hope this helps...