Firstly the update virus database is an option that you can either enable (default) or disable for Real Time, Manual or Scheduled scanning.
The problem with the actual AV updating is probably due to an previous AV update that failed to work correctly and has become hung (I’ve only seen this happen with multiple manual updates myself). From More button in any event log you can reach CIS’s external log viewer and check the Tasks Launched to confirm the failure of any AV updates. This being case, it does seem that a system reboot is the only way to resolve this problem.
OK, I suspect that you’re not normally able to hide the AV update pop-up when the update is being performed automatically. I can’t test this myself as the pop-up only appears on the screen very briefly (if at all) when an automatic AV update is being performed. I can only assume that your AV updates are a lot slower than mine for some reason. Am I right in assuming that this pop-up doesn’t remain on your screen for long?
External Log Viewer: Yes, CIS’s external log viewer window (as do all of CIS’s windows) remembers its size & position from the last use. This is in-line with Windows as a whole, I consider this desirable (if it would only remember the column sizes as well)… why is this a problem for you?
Restore down function appears to not restore down if closed while maximized and reopened, but you can still reset it to your size/ratio preference by clicking restore down and then dragging the window to your preference from the bottom right corner. See screenshot.