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One day, a few weeks ago, my computer simply stopped saving my settings when it shut down. When I boot up, shortcuts I've put in the start up folder and window positions (such as IM clients) have changed back to how they were a few weeks ago. I makes no sense to me. I was playing around with some boot-time speeding tricks, but none of them should have done this. I checked over them just now.

I know I'm being vague...

And I can re-do these things on restart every day...but slowly the changes are piling up.

Okay, this is really weird...if I put TWO shortcuts to the program in the startup folder, the program will run, but it will delete its shortcut...???

Can you list what tweaks you used , or post a link to it? And did you also use shutdown tweaks like enabling "fast shutdown" or something like that?

'msconfig', which is built into windows. You can access it via 'run' in the start menu.
Also TweakUI, which is hidden on the microsoft website somewhere...

I'll check my shutdown options. Good thinking.

What did you disable with msconfig?

And the tweakui tool indeed has a fast shutdown tweak afaik , that could be responsible for loosing settings.

All the diasabled programs in msconfig are not system programs. I left the confusing ones and only disabled what I could identify as something I had installed myself and didn't need.

Checking TweakUI now trying to find where they hid the 'fast shutdown' option...

I found no 'fast shutdown' option.
But randomly digging around, I seem to have 'knocked something loose' by accident. 'Cause it's working now. Wild. Oh well. Who needs a reason? It's working. That's good enough for me.