I go to tools/options/security and put a check in "remember passwords", and the next time I go to the same place there is no check.
Firefox does not remember that I have put a check in the Remember passwords box.
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did all that. Still no remember, and checkmark still goes away.
Are you browsing in Private Browsing mode by any chance? See: Private Browsing - Use Firefox without saving history
No, it isn't in private browsing.
Please see: Remember passwords for sites just in case you're missing something.
The remember passwords box still reverts to empty after I put a check in it.
Which security software (firewall) do you have?
Some can lock privacy and security settings in Firefox.
The only change I have made to my computer was to install Firefox 4.0.1. Nothing else changed. Therefore, how can it be somet5hing outside of Firefox? Before the upgrade everything worked perfectly, with my passwords being remembered for at least 90% of the applications that I use.
A firewall treats each new program as untrusted and if you didn't specifically allowed Firefox then that firewall can use some default settings.
So it is worth to check any advanced settings in the firewall or anti-virus software.
Websites remembering you and automatically log you in is stored in a cookie.
Do not use Delete browsing, search and download history on Firefox to clear the "Cookies" and the "Site Preferences"
Clearing "Site Preferences" clears all exceptions for cookies, images, pop-up windows, software installation, and passwords.