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Last weekend I downloaded security patches from microsoft. After installation was done I was prompted to reboot. System rebooted in command prompt. I'm not that computer saavy. I know enough about command prompt to know I don't know how to use it. I couldn't figure out how to get out of command prompt, so I pressed my restart button. Went through reboot again, this time in Normal mode. In the middle of reboot got a blue screen with a message that something in the registry failed and to repair it the system replaced the registry file with an earlier one.
When the system was fully booted I got a flurry of "New hardware found" messages concerning hardware that I installed a month ago, was prompted to insert my W98SE startup cd. Followed the instructions, got a flurry of can't find this file, can't find that file messages. After all that it seemed like the system was finally back to normal, but quickly found out it's not. My McAfee Security Center won't open and gives me components missing or not installed properly messages. I can't hotsync my PDA (which was installed 3 years ago), and whenever I try to hotsync I get messages about my COM1 port being unavailable, even though the device manager says COM1 is working properly. I can't open my Palm desktop software, I get a message about improper configuration. And everytime I boot up I get messages that the system is trying to launch two Norton Antivirus files that were removed when I uninstalled Norton months ago to replace it with McAfee.
After looking for similar problems in the forum, I tried scanreg/restore, and found a list of scanreg files from 2001, with the current one being from this month -- so if I replace the current one with an earlier one, it will probably be an even bigger mess.
Can this problem be fixed? If so, how?
Thanks.

Yeah, it looks like it restored a very old registry, one from before you added all the hardware and software. You may have had the scanreg option in msconfig--startup unchecked so that no backups were created. In that case the old ones would have been kept instead of being overwritten.
If you have a registry restore date from this month it probably won't hurt to try it, although that may be the one that was just restored.
Otherwise, the only thing to do is reinstall all the software since even though the files may be there, the registry has no reference to them.

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