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The first problem sounds like you are either crashing out every time, or you don't have write permission, which seems unlikey.
The second one, go to Options/View and look at View Transition.
Okay, that fixed the view transition setting but the background color still won't stay set.
These settings are both in system options and I made some other changes in there also. All the other changes stayed after a shutdown and startup except the background color.
The "background color" problem you describe sounds like an issue that we fixed in 2008 SP5.
The issue was caused by our "Welcome to SolidWorks" dialog for users who selected the:
"I am a new user. Show quick tips help to get me started" option...
Selecting the option above, flags you as a "new user" in the registry until the next major version of SolidWorks (HKCU/solidworks/solidworks 2008/general/userExperienceLevel). This "new user" flag was causing this particular issue.