On your console look at the Policies tab / Hash Control section. Set the search criteria as Endpoint IS (machine being scanned) and VERDICT ISN'T BENIGN then click search. This will return all of the hashes that are not benign from that machine and the status of wildfire uploads of them. This should at least give you a way to see where the ESM server is in evaluating the hashes. I believe I may have experienced something similar a while ago. I had to open the TRAPS AGENT console on the endpoint, check in, close the TRAPS console on the agent, wait a couple minutes and then start the process of running the CYTOOL followed by the TRAPS VDI TOOL. That ensured that the local agent had made a successful connection to the ESM before running the tool.
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