I am still seeing at least 2 issues, related to some of the other user accounts. There are 5 accounts total on this pc, all of them are administrator accounts. I believe 3 of them have never (or seldom) been used, 1 is used occasionally, and 1 is used frequently. What I am seeing:
All the instructions I did in this thread were done under a single account. This account appears to be running normally.
On the other 4 accounts, windows appears to have lost some information about some executable programs. I notice that when I log into these accounts, there are some icons which I expect to appear in the taskbar (MSE, ooVoo, skype, etc) which do not. When I try to start these programs manually (click on start>AllPrograms>Microsoft Security Essentials) it asks me to choose the program I want to use to open this file, and gives me a list of files to choose from. It does the same thing with MBAM, ooVoo, and several other programs. Other programs (IE8) seem to start just fine.
On the frequently used account, there is an additional problem related to internet connection with IE8. IE8 cannot seem to find any websites.
OK, reran MBAM under each account, found the following:
-the problem I was seeing with windows not finding executables was caused by a registry modification to HKEY_CLASSES_ROOT\exefile\shell\open\command\{default}. This was found and corrected by MBAM.
MBAM also found 2 additional problems, 1 was related to the file c:\windows\system32\memping.dll and the second I was not able to write down. MBAM was able to fix both of these.
The problem I was seeing with IE8 not able to connect to any websites under one account was related to a LAN configuration setting in IE which was set to use a proxy server. I found this on my own - figured it had to be related to internet options settings because 4 user accounts were able to access the internet and one was not. Fixed it by opening IE8, selecting tools>internet options>connections tab>LAN settings and unchecking the "use proxy" dialog box. This account is now able to access websites again.
As a last step I reran MBAM and MSE and both ran without error. Everything appears to be stable and running clean.
No more to report on my end, please feel free to close this thread if you think we are done.
Thanks again for your help, I really appreciate it.