I have the same problem - on my laptop, I have Windows Vista Home Premium (32 bit), and whenever I run WindowBlinds 6, Aero is disabled when I bring the laptop from standby mode or whenever I reboot. When I go to Preferences on the desktop, I get the classic preferences pane, and not the new webby one, and the only choices are Windows Classic and Windows Aero Basic. When I try to apply Aero through WB 6, it just goes to Aero Basic. The only way I can enable Aero again is to unload WB 6 and then reboot. It's still installed on the laptop but I don't use it anymore because it keeps wrecking Aero.
This is all as it should be. Windowblinds is an in depth Theme manager with it's own type of themes. If you apply a theme through windowblinds then YES aero is no longer in effect, you now have a Windowblinds theme applied. If you go into personalize and change it back to aero then you are causeing a conflict with windowblinds.
If you want aero then like above posts state start the Windowblincs interface and scroll the list of themes all the way to the left and choose windows aero and your Aero theme will be back when you apply it.
On another note if you want to combine aero like window frames and stuff with window blinds there is options to do this THROUGH the Windowblinds interface. Take some time and look at all the settings in WindowBlinds.
If you only want Aero and no other Windowblinds features then it would be best to uninstall Windowblinds all together.
I don't know how much this helped but I hope at least some.
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