Yeah John, that is normal for me in X2. If I'm not mistaken, a new plugin manager was given to us in the last update patch. It fixed some things and sort of hindered a few others. Like for example, other than the issue you are reporting, if I use the browser for my plugs where I can drag and drop them, the plugs are either missing from there yet are visible if I right click on my FX bin, or vice versa in that they will be visible in plug browser and not visible if I right click on the FX bin. Uusually a restart of Sonar upon installing new plugs fixes this...but there have been a few times where even that seemed to not work and they "just showed up" eventually.
I've reported this issue and believe either Noel or one of the other bakers mentioned they were aware of it. Now, what HAS worked for me that you may want to try if you haven't....go to your plug scan in Sonar preferences, NOT plug manager. Press "reset all" button, put the check in the box to rescan all plugs and then do a scan. After the scan is done, take the check out of "rescan all plugs" so it doesn't take forever to load. You pretty much need to do this one time if you haven't and you should see an improvement with pluging manager. This should stop the restarting most of the time, but you may have to still restart if a plug doesn't appear.
I use custom plug menu's with my auto scan set to off. The reason being, I like to manually scan the plug so I can add it to my menu. This also stops me from installing several plugs in one shot this way I never miss any and forget what was installed. :)
-Danny