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Admin Tools does not –and, honestly, cannot– touch your menu at all.

Supposing that you are talking about the Components menu, the only place where Admin Tools appears (on a menu item added by Joomla! itself) the "item reordering" happens for at least 3 and a half years and has nothing to do with Admin Tools and everything to do with the way Joomla! 2.5 orders its menu items, something considered a bug and fixed in Joomla! 3. Joomla! 2.5 will order the Components menu items based on their translation key as seen in the title column of the #__menu table where the level column equals 1.

As you can see, all Joomla! core components and all properly written components have a title which begins with COM_. Some components have menu items whose title does not begin with COM_. Therefore, the COM_ items will appear first and the other items whose first letter comes after C will appear next. This works well when the language is English and all components' menu items' title begins with COM_. Things get funky when you are using a different language and/or when you have items with titles not beginning with COM_.

As I said, this was considered a bug and was fixed in Joomla! 3. Joomla! 3 will order the component menu items based on the translated title. Also as I said this has been the case for several years and has nothing to do with Admin Tools itself. It's how Joomla! works. If you upgrade to Joomla! 3 which fixed this bug you will see that your menu items work just fine.