There is absolutely no need to go into plugin manager and manually launch the scan if you have automatic background scan on. That workflow is no longer needed in X3. As long as you have the VST scan paths set up to point to the right scan folders, SONAR will automatically detect when new plugins are added and scan them in the background. In fact if you launch it from plugin manager while an automatic scan is already running from X3 that might explain the multiple launches.
Also its a pretty rare case that you need rescan existing plugins enabled. Why are you leaving that on permanently?
Doing that will make the scan run really slow since it does *every* plugin each time the scan is launched. If you have > 500 plugins of course that will take time since its loading every one of them.
Now regarding the automatic background scan, the only time that runs is once on startup and then subsequently *only* if something changes externally to the vst scan path folders. Is it possible that something you have is adding or updating files within those folders? If so that will retrigger the background scan. From the symptoms described it looks like that's whats happening.
In general the default values in the VST settings should handle 99% of the use cases so you should only change them if you need to. If you don't wish the automatic background scanning set the scan option to "Scan On Startup". Then SONAR will only trigger the scan once when SONAR is launched (it will still be done in the background)