Sounds like there is definitely a problem with Visual Studio retaining your settings between round-trips and possibly your Visual Studio settings profile in general.
The solution I’d recommend is firstly to reset all settings, secondly customize things to your personal preference and finally take a backup of those customized settings. The idea is that this settings backup file can be used later to automate a quick settings restore to a point you are happy with. The following steps show how to do this and hopefully should sort out even the most confused Visual Studio setting issues:
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Close down all instances of Visual Studio.
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Go to Start > Programs > Visual Studio 200X > Visual Studio Tools > and choose ‘Visual Studio 200X Command Prompt’
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Run the sligthly less well known ‘devenv.exe /ResetUserData’ command. With this command you will lose all of your Visual Studio environment settings and customizations. Because of this, the /ResetUserData switch is not officially supported and Microsoft does not advertise it (the switch is not described in the help for devenv.exe you get when you type devenv.exe /? in a command prompt). Importantly, wait for the resulting devenv.exe process to disappear from Task Manager or even better Process Explorer.
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When the process disappears from Task Manager or Process Explorer, run ‘devenv.exe /ResetSettings’ which will restore the IDE’s default settings and eventually start a single instance of Visual Studio.
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Now in Visual Studio choose ‘Import and Export Settings…’ near the bottom of the ‘Tools’ menu to start the Import and Export Settings Wizard.
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Choose ‘Reset all settings’ radio button and Next > Choose ‘No, just reset settings, overwriting my current settings’ and Next > Choose your personal ‘Settings Collection’ preference, I would choose Visual C# Development Settings here (Note: What you choose here has an effect on keyboard shortcuts etc. but you can always repeat this process until happy) and click Finish.
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When you get the message that ‘Your settings were successfully reset to XXXXXX Development Settings.’ click Close then spend a good bit of time adding any personal customizations to Visual Studio such as opening windows you always want open, customizing toolbars and adding any toolbar buttons etc.
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When you are finished with your personal customization and completely happy with your setup go again to Tools > ‘Import and Export Settings…’
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Choose ‘Export selected environment settings’ radio button and Next > Tick ‘All Settings’ and Next > Choose a file name and directory and click Finish to store a backup of your current settings in a .vssettings file.
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In future if things go haywire again head back to Tools > ‘Import and Export Settings…’ and this time choose ‘Import selected environment settings’ radio button and Next > Choose ‘No, just import new settings, overwriting my current settings’ and Next > Either choose the name of your .vssettings file from the list (usually under the My Settings folder) or Browse.. to where you saved the file and Next > Tick ‘All Settings’ and click Finish.
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Importantly, close the single instance of Visual Studio. Any future instance you open should retain your latest customizations.