Say I had a a logo which was black+orange, over white and this was used on the website. What if, in the "control panel" area once users log in, there is a different layout and as a result the colors of the logo change to gray+orange over black? Same logo, just different colors. Is that okay or should I work to keep the logo the EXACT same always?
That all depends on your intentional "branding". If you plan to use the brand of the shape more than the colors... OK. If the colors are important to your "brand"... then No. Sometimes the color changes on a site "logo" can be used to let the user know they are in a different section or category of the site. It all depends on you. IMHO.
Depends also on your reason for having it changed once the user logs in. Is it just because the layout changes? Seems like there should be a reason for doing so other than just because. But if the logo is recognizable enough, a reversal in color could still be okay.