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In the past week, I have been presented with 3 machines (2 with WinME and 1 with W98SE) that are massivly infested with Winpup. With a copy of Adaware/Hijackthis and manual removal, I have been able to remove all iterations of this POS, and also I have removed it from the registry.
However, on the W98 machine, MSConfig still shows the 96 iterations of the program that were originally in the startup sequence.
I seem to have 2 options. I can simply leave them unchecked and run in the selective startup mode, the only drawbacks of which are that it offends my sensibilities and it takes MSConfig about 2 full minutes to load, or I can run in the normal mode and cancel 96 "missing program" dialogs as the machine boots.
WinME had a "cleanup" button that removed them, but 98 does not. I have searched thoroughly, and am certain they are no longer on the machine nor in the registry, only in MSConfig.
Neither TweakUI nor Codestuff's Starter program have a tool that will remove them. My current thought is to try to graft a copy of WinME's MSConfig onto W98 and try it that way. Any other thoughts?
Thanks, CJon

Entries left behing in msconfig startup can be removed by doing the following:
click start,run, and type regedit
open HKEY_LOCAL_MACHINE
Within that registry open the following:
software
microsoft
windows
current version
Under current version look for the following:
run
run-
runservices
runservices-
Here you will find the items that are in your startup tab.The ones with the[-] are unchecked in your startup and the others would be the the ones you have checked for startup.You can delete the ones left over that you don't have on your system anymore.Also check HKEY_CURRENT_USER under the same folders.Hope this helps.

Things that remove dead MSConfig items without tinkering with the registry:
StartupCop
SystemMechanic (free trial download)
EasyCleanerI'm sure there are lots more. How about others adding to this list?

I listed all the sources I could think of that load in msconfig and how to remove them on this thread:
http://computing.net/windows95/wwwboard/forum/155414.html
Some of it overlaps what wiked_wrathchyld (whatever happened to just Bob or Tim?) wrote.

Startup Control Panel (free)
www.mlin.netStartup Cop v1.1 (not free; no trial download)
www.pcmag.com/article2/0,1759,2173,00.aspSrartup Cop Pro v1.02 (not free; no trial download)
http://www.pcmag.com/article2/0,1759,1554244,00.aspSystem Mechanic 4 ($50; free trial download)
Very good; many functions; pricey
http://www.iolo.com/downloads.cfm

Turns out that when I went back to a normal startup in MSConfig and then fought through the 96 "missing shortcut" messages to a normal boot, I was then able to delete all of those items with Codestuff's Starter. I probably could have done the same with Mike Lin's StartupCPL. When I rebooted, they were gone.
This, even though they did not show in any of the -run registry keys that would indicate they were disabled by MSConfig. Go figure.
Anyway, thanks for the help. I can recommend Starter to the list of free startup editors. It seems to work OK. Available here:
http://freedownloadswindows.com/windows/download/69276/Starter.html

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