BOINC FAQ: Running BOINC On Microsoft WindowsÂ®
From Unofficial BOINC Wiki
 Can I install the BOINC Software as a service?
Yes you can. With the Windows Installer program, that is the first question that is asked. Select the bottom option.
 I have the BOINC Software installed but when I minimize the window I get another program listed in my Taskbar, how can I get rid of that pesky thing?
If you use the "minimize" control on the window frame you indeed get a situation that looks like what is shown in this picture. The minimized program closes and then creates an entry within the Taskbar and can be reactivated and opened simply by clicking on the tile for the BOINC Manager. For additional information on this feature you can read more about it in the BOINC Application Owner's Manual.
To make is so the tile is not visible, use the "Hide" (or "Close") menu item under the "File Menu". When that option, or as an alternative, using the "Close" control (the big red "X") on the window's Title Bar, you will get the BOINC Icon only showing in the Notification Area. To learn more about this subject you should refer to the BOINC Application Owner's Manual.
 I don't see the BOINC icon in the Notification Area of the Taskbar. Where did it go?
If you have not clicked on, or opened the BOINC Manager for some time, Microsoft Windows® will sometimes "hide" the icons that it feels that you have not used enough to keep them visible. This does make sense in that it keeps the Taskbar to the smallest possible size and allowing the most effective use of the space. I do not have a good picture right now, because I am always fiddling with the BOINC Manager. But the first example I show the "Notification Area" when it is closed.
A depiction of the Notification Area on the Taskbar for Microsoft WindowsÂ® as it is displayed on the screen.
In the second example here I show the same area with the "Notification Area" open with all of the icons visible.
All you have to do is to click on the "<" symbol and you will be shown all of the icons that are available within the Notification Area of the Taskbar. To cover up the icons again the ">" symbol can be clicked. In the mean time, if you have clicked on the uncovered icon of BOINC you should start to see it within the Notification Area all of the time now. Well, until you wait too long to show the BOINC Control Panel's window, then you will have to look for it again. But now you know where to look!
Also, complements of Skip Guenter:
This can also be a general windows problem. I see it regularly and especially on machines that have many started app icons (firewall, antivirus, UPS monitor, mbm, spybot, lan connect, freeram, webcam, BOINC, etc. etc.)
Often systray icons will not appear (when the app is autostarted at boot) when initiated from a cold start or warm restart. As I understand it this has to do with all that windows is trying to get done at that point (device drivers, services starting, etc. etc.). It's running, but the icon is not to be seen. I have found that logging off an d back on will usually resolve the systray icon display.
 How do I get access to the BOINC Manager? All I can see is the icon in the "Notification" Area.
One of the more interesting things that you can do with this icon is to right-click on the icon and you will get a pop-up menu that can do a number of things for you.
If you just want to open the window for the BOINC Manager, you can double-click on the icon, or select the menu with a right-click on the icon and then select "Show" menu item.
As shown in the example, the Pop-Up Menu has roughly the same controls that you have available on the File Menu. Right-click on the BOINC Icon and you should get a pop-up menu that has the "Show" option.
If the "Show" menu option is not available (grey color), then you already have the BOINC Manager window open somewhere. Now all you have to do is to find out where you left it.
One of the other options that is useful here (while I have your attention) is this is where you can also "suspend" the BOINC Software so it does no processing until you restart it. This is especially useful for those occasions where you don't want to shut it down completely.