Sorry to hear about those issues.. Depending on the maintence agreements, you should contact the appropriate support channels and get a ticket logged on this issue so it can be resolved..
An issue/annoyance I see a lot with TelnetCE on the WT41N0 is that by default, TelnetCE will prompt you if you would like to use the Bluetooth Scanner with a pop up window. If you are using the tethered scanner you have to set it as the Default Scanner in the emulation parameters on the device, otherwise it will always give you the option to use the bluetooth scanner.
The issues that you are experiencing with the emulator suddenly closing - Do they seem like TelnetCE is crashing or is it more like your telnet session is just closing? If you're losing connectivity temporarily on the devices and you have the "Exit On Disconnect" Emulation Parameter set the TelnetCE application could be closing every time your device roams out of wireless coverage.
Sorry Jmdermody but it is not the right answer
I am agree with Jreed, on WT41N0 the scanner suddenly stop working
we are in trouble on a lot of customer
Have you tried updating to the latest OSUpdate and SPRs provided by Motorola. If you're having scanner issues that should be the first place you should look.