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In this particular case, it's a crash dialog, and the only solution would be to resolve the cause of the crash.
What sort of dialogs are you referring to? I have never experienced the issue of some dialog requiring user input being displayed when invoking VC 6 or VS.NET 7.x via the command-line.
In VC6, I do recall disabling the VSS integration by creating a DWORD registry value HKEY_CURRENT_USER\Software\Microsoft\Devstudio\6.0 \Source Control\Disabled = 1, but I thought that was only to prevent popups when interacting with the IDE (not the command-line). If the dialogs you're seeing are related to that, there may be a similar registry setting that would help.
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