Manually added tools through the Administration Workspace->Sites tool, which isn't listed in the list of tools in Site Info->Edit Tools, get removed when a user goes in to Site Info->Edit Tools and makes changes.
To reproduce (in trunk)
-Create a site
Go to Administration Workspace>Site Tools and find the new site
Add a tool to that site which isn't listed in the Site Info>Edit Tools list (in trunk, I picked Lessons since it wasn't in the list)
-Go to the new site, notice that your tool you added is there
Go to Site Info>Edit Tools and just click save (notice that the tool you added isn't listed)
-After saving, you will see that the tool is now removed from the site.