I can only think of 3 reasons something like this would happen.
 
First you got a virus of some sort. since your computer is not connected to the internet I doubt that is the case. but run a scan anyway. I don't think the plugin install would insert a virus. especially if you paid money for them. A corrupt partition is not likely to affect the time and date settings. 
 
Second somebody who knows you got on your computer and played around. Once again highly unlikely but you never know.
 
Third some how your CMOS/BIOS was reset. If this is the case then re-formating your hard drive and installing your operating system won't change much. It will give you a lot of extra work. This seems to be the most logical solution to me.
 
It could be that your CMOS battery is dying but it is not totally dead. If the date is changed and the time is different and the reboot sequence is set to default, then this is more than likely a BIOS issue. a problem with the battery would be the first thing I look at. these batteries are cheap and I would just replace it.
 
As for not being able to read the USB thumb drive I would look at your USB settings in the bios screen. More then likely there is a default setting that changed something. Maybe that is preventing your computer from looking at certain files on your thumb drive. That is my best guess.
 
Be sure and check the thumb drive on a different computers to see if it works. I have had this issue before and as I recall during the troubleshooting process, I installed the program in question on another computer and then checked the usb stick to see if it would unlock the program. I discovered that even though the file was on the thumb drive it became corrupt and it would not unlock the program. See if it unlocks the program on another computer.

Marcus Curtis
I can only think of 3 reasons something like this would happen.
 
First you got a virus of some sort. since your computer is not connected to the internet I doubt that is the case. but run a scan anyway. I don't think the plugin install would insert a virus. especially if you paid money for them. A corrupt partition is not likely to affect the time and date settings. 
 
Second somebody who knows you got on your computer and played around. Once again highly unlikely but you never know.
 
Third some how your CMOS/BIOS was reset. If this is the case then re-formating your hard drive and installing your operating system won't change much. It will give you a lot of extra work. This seems to be the most logical solution to me.
 
It could be that your CMOS battery is dying but it is not totally dead. If the date is changed and the time is different and the reboot sequence is set to default, then this is more than likely a BIOS issue. a problem with the battery would be the first thing I look at. these batteries are cheap and I would just replace it.
 
As for not being able to read the USB thumb drive I would look at your USB settings in the bios screen. More then likely there is a default setting that changed something. Maybe that is preventing your computer from looking at certain files on your thumb drive. That is my best guess.
 
Be sure and check the thumb drive on a different computers to see if it works. I have had this issue before and as I recall during the troubleshooting process, I installed the program in question on another computer and then checked the usb stick to see if it would unlock the program. I discovered that even though the file was on the thumb drive it became corrupt and it would not unlock the program. See if it unlocks the program on another computer.

Thanks for your reply Marcus. I did install the Waves license center on another computer and it showed the licenses. The CMOS battery.does appear to be dead, as every time I cut power to the computer, the time resets and the BIOS settings change. So I guess I'll start with a new battery and go from there.
Thanks to everyone for your help. I'll post again after replacing the battery to let you know how it goes. Thanks again!

Good news! I replaced the battery, made some changes in BIOS, ran the Windows 7 repair utility, uninstalled Waves, and got rid of everything in the registry that had anything to do with Waves. I reinstalled it, then ran Sonar and the VST scan picked it up immediately! Everything is great now. Thank you all so much for your advice! This forum rocks!!!

Great! Did you get rid of the crysonic software?

I tried a system restore a couple days ago, so that got rid if them. Don't know if I'll try installing them again or not. Thanks again.

FWIW, I had a problem this last weekend (possibly storm-related), where my Waves licenses were no longer found. It turned out, I moved the USB hub over to a USB2.0 (from 3.0) and Sonar could see the Waves license files.
 
Sidenote: If you pay for Waves WUP, don't hesitate to call them. You're paying for it, so use the support.

brconflict
FWIW, I had a problem this last weekend (possibly storm-related), where my Waves licenses were no longer found. It turned out, I moved the USB hub over to a USB2.0 (from 3.0) and Sonar could see the Waves license files.
 
Sidenote: If you pay for Waves WUP, don't hesitate to call them. You're paying for it, so use the support.

Thanks for the tip brconflict. I did try every USB port. I don't even have any 3.0 ports. Time for an upgrade???

For what else it is worth. I have my licenses stored on my PC. I disabled the Ethernet card and enabled my wireless network adapter so I could try a wireless control program from my ipad.
 
When I opened Sonar the scan said the wave licenses could not be found. As soon as I enabled the Ethernet card it was able to scan and find the licenses. So if I want to use my wireless adapter instead of the Ethernet card the waves stuff won't work... Probably have others that have in some way been tied to the Ethernet card I just have not found them yet.

Windows activation is tied to the ethernet interface MAC number (amongst other things) so it wouldn't surprise me if other software used the same concept.
 
You can actually run the ethernet and the PC wi-fi at the same time. Network IP addresses are not one per computer but one per network interface, so the ethernet and wireless need different IP address numbers but after that it should work, though you may get some "interesting" network routing going on.
 
I use V-Control Pro on the iPad  with Sonar without the PC having wireless enabled due to the  PCI bus latency problems wireless networking usually intorduces which causes drop-outs in Sonar. I have the DAW ethernet wired to the router then the iPad connects to the router by the iPad's internal wi-fi. Works fine.

Thanks for that info tlw! I will play with this some more.