Issue: When you start Desktop Manager, you get the "Checking Application Updates..." popup, even though you have un-installed the App updater. This can take up to 30 seconds before you can sync.
Edit the file <deviceid>.xml located here:
C:\Documents and Settings\<username>\Application Data\Research In Motion\BlackBerry\Loader History
where <deviceid> = your device ID and <username>= is your windows username.
Delete the following line:
where XXX = your vendor ID.
Save the file and the DM no longer checks for app updates.