According to the CPUU Administrator Guide it's best to set 'Reset Outlook junk e-mail options' in the CPUU config as CPUU does not process these settings and after profile processing those settings won't work for the target mailbox in most cases.
In this case, CPUU isn't clearing the senders lists but the lists are most likely blank because the senders haven't been explicitly matched by the DSA.
See the following note on page 7 of the CPUU Administrator guide:
"CPUU also clears the junk e-mail settings if the Reset Outlook junk e-mail options for target mailbox option
is selected in the Configuration wizard. Otherwise, the settings will remain unchanged and may not work
properly for the target mailbox."