Take a look at logging from the upload process to see if it gives any indication of a problem. This logging can be found in the %TEMP%\ManageSoft\uploader.log file, where %TEMP% is the temporary directory of the user that FlexNet scheduled tasks are configured to run as. This will often be C:\Windows\Temp on beacons, as scheduled tasks are often configured to run under the SYSTEM identity on these servers.
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