RT templates and others may be effected because of missing Menu_Item_Root in J2.5.4 (***_menu) table.
Not sure if this is unique to Joomla ***_menu table as from J2.5.4 onwards, but this is the problem I encountered.
After migrating to J2.5.4 from J1.5 using jUpgrade component, the ***_menu table no longer has a Menu_Item_Root with an id (1).
This caused the following error when trying to save new menu items. This was the error:
Save failed with the following error: MenusTableMenu: :_getNode Failed -
The only way round this was to create a new line in the ***_menu table in phpMyAdmin.
To do this, open ***_menu, click on (Insert) and enter the details as shown in the attached image. Then click on the (Go) button to insert the new line with an id (1).
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Go back into your Joomla admin and open each menu, select all menu items and then click on the (Rebuild) button. Do this for all menus.
Problem solved.
Always back up first.
PS
I also noticed that a fresh install of J2.5.4 had the same problem so this is not unique to the upgrade