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Losing application settings

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SOHO1:
I recently encountered a problem where my boot times became HUGE with 90 min to 120 min reboots.  After extensive research, I found that tweaking.com helped another user with the problem INDEED IT HELPED ME TOO! Kudos! However, I find that a new problem seems to be occurring and I don't know if it relates to Tweaking or not.  I am losing various settings when I reboot.  Chrome and IE "forget" all my accounts and passwords that they normally remember for sites.  Other strange little things too, like which power configuration I am using (should be custom instead of the default).  Might tweaking be doing/installed/configured/ something to reset these every boot?  How can I track this down?

Boggin:
I've passed this onto Shane.

Julian:
no it should not effect any of those settings. what 3rd party programs do you use?

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