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A DOS window pops up every time an ArcSDE connection is made.
If you see a DOS window pop up each time you establish an ArcSDE connection, you have probably checked the 'Allow service to interact with desktop' checkbox in the ArcSDE service properties.
As long as you keep the DOS window open, the ArcSDE connection will be fine; however, if you close the DOS window the ArcSDE connection will end. For example, in ArcCatalog you will receive a 'Network I/O' error the next time you attempt to preview any Object Class or Feature Class via the connection.
To eliminate this DOS pop-up window: