The problem is in your DLL.XML file. It's the file that tells FSX what add-ons to use. So to fix the problem your going to have to edit it.
Make sure you can view "hidden files".
Go to C:\Documents and Settings\"Owner"\Application Data\Microsoft\FSX
In there you will see the dll.xml file.
Make a copy if it and save it to your desktop. This way if something goes wrong later you can fix it.
Right-click on the original and open it with Wordpad.
You will see something like this:
<?xml version="1.0" encoding="Windows-1252"?>
<SimBase.Document Type="Launch" version="1,0">
<Descr>Launch</Descr>
<Filename>dll.xml</Filename>
<Disabled>False</Disabled>
<Launch.ManualLoad>False</Launch.ManualLoad>
<Launch.Addon>
<Name>Object Placement Tool</Name>
<Disabled>False</Disabled>
<ManualLoad>False</ManualLoad>
<Path>..\Microsoft Flight Simulator X SDK\SDK\Mission Creation Kit\object_placement.dll</Path>
</Launch.Addon>
<Launch.Addon>
<Name>Traffic Toolbox</Name>
<Disabled>False</Disabled>
<ManualLoad>False</ManualLoad>
<Path>..\Microsoft Flight Simulator X SDK\SDK\Environment Kit\Traffic Toolbox SDK\traffictoolbox.dll</Path>
</Launch.Addon>
<Launch.Addon>
<Name>Visual Effects Tool</Name>
<Disabled>False</Disabled>
<ManualLoad>False</ManualLoad>
<Path>..\Microsoft Flight Simulator X SDK\SDK\Environment Kit\Special Effects SDK\visualfxtool.dll</Path>
</Launch.Addon>
<Launch.Addon><Name>FS Recorder Module</Name><Disabled>False</Disabled><ManualLoad>False</ManualLoad><Path>C:\Program Files\FS Recorder for FSX\RecorderFSX.dll</Path></Launch.Addon></SimBase.Document>
In fact you should see exactly that. So, having made a backup copy of the dll.xml to your desktop, Cut and Paste the red text above and replace the text in the original dll.xml. Save it and close it out. Then go fly in FSX and see if you get the "Tools" option.
If not, replace the copy of the original dll.xml that you have on your desktop back into its original folder, start pulling your hair out, and kick the computer. That might work too.