I don’t know why “webmin-virtualmin-nginx” is in there. I imagine it’s an update for those who use it. As long as the process isn’t running, the files won’t make any difference other than taking up a tiny bit of room.
As for the staff support, I’m not certain that this is a Virtualmin problem (nor that it isn’t); but I lean toward it’s being a coincidence of timing. Otherwise we’d have a bazillion people with the same problem after the update.
Richard