I'm assuming you're using a WT4090, WT41N0, or another device that does not have a built in scanner by default. To prevent the pop up window from appearing every time TelnetCE launches, specify a Default Scanner in the Emulation Parameters of TelnetCE. You will have to specify this within the desktop configurator for Emulation Parameters as this cannot be set manually on the device itself. If you are using a tethered scanner like a RS409 or RS419 then specify "Serial Scanner" as the preferred Default Scanner. The parameter seems to be case sensitive from my experience so be sure to type in Serial Scanner exactly as it appears. The other options for Default Scanner values can be found within the description for the Emulation Parameter.
As you can see in this screenshot below, the default value for this setting is "Ask the User", which refers directly to the pop up window that you are being presented with when launching TelnetCE,
