OK even more weird behavior at home, so a little info first.
At work (where I first posted and described this issue) I am running 10.7 Lion.
At home (where I am while writing this post) I am on 10.8 Mountain Lion.
With respect to Launch in the Background, yes it is enabled (at both work and home)
While here at home (10.8) Stop Workers and Agents both say "(0)" and are greyed out. I can check work tomorrow but would expect the same. I have never intentionally used 'agents' and don't really know what they are. I use the program in what you used to call the URL Manger Pro method.
I receive the Update available notice either when I boot my machine and Bookmacster launches or when I select "Show Bookmacster". So, I guess answer would be that it occurs either while it is running or as it is launching.
With respect to getting the additional "installing" message, I know it has occurred for at least two of the updates. Not sure about the others.
When I got home and got on my computer (already booted, just asleep) and picked "Show Bookmacster" in order to answer your questions, I got the update notification for 1.16.3. I chose to not install it right now as I noticed that I had two menu items already and wanted to investigate. One of them indicates it is 1.16.1 and the other is 1.16.2.
Now, here is the strange behavior and is different from what is occurring on my work computer:
On my work computer (10.7) when I chose "Show Bookmacster" from either of the menu items, it appears to open the same window. I can tell no difference. I can go back and forth between the menu items selecting "Show Bookmacster" and it keeps the same window in front.
However, here at home (10.8), when I chose to "Show Bookmacster", each one opened a different occurrence of what appears to be the same window bookmark file (appears to be the same content). What is really strange is that, as I sit here typing this, these two window keep repeatedly, one after the other, coming forward, one at a time, and saying "no duplicates found". If the bookmark files are in the front, it occurs about every 24 seconds but if they are pushed behind another widow (like Safari as I am typing this), it seems to occur every 12 seconds (these times are not exact, just me counting
I have attached a movie. You will notice I move some of the windows. This is because, after a couple of iterations, the two windows will be on top of each other and I wanted you to see both.
Oh, one last thing. I do not know for sure if I have check for duplicates turned on at work. I will check tomorrow.
Regards,