Thanks for the help Gustabo

Sorry, I'm being very needy but it still doesn't seem to work... After uninstalling it, I right clicked on the program called "Install AmpliTube", clicked on the option Run as Administrator (no option for Install as Administrator...), it installed normally but when trying to use it in Sonar it has the same problem... I'm beginning to wonder if the versions I have aren't compatible (the free version of AmpliTube 3, and Sonar x1 LE)
 

Sorry if this question sounds too obvious, but are you installing the stand-alone app, and does the plug-in require some other action? It says on their website:
 
 

When you download and register/authorize the software, you'll get a fully functioning "standalone" app with a built-in 4-track recorder, plus you get the plug-in version for your favorite DAW. No matter what your computing platform (Mac/Win),

I think you are right! After looking into the specs on the website, it seems that Aplitube app isn't the thing that runs as a plugin, the thing that can run as a plugin is in fact the Custom Shop, which isn't actually a guitar amp emulator... 

Custom Shop is actually a part of Amplitube 3! The stand-alone version of Amplitube 3 should show on your desktop. Make sure you have an internet connection. It's much easier to authorize with that. You must authorize it by going to the My Account section of the IK Multimedia page first. If you haven't done that go there and it will have a list of products you have registered on that site. You will see the authorization number for your download listed on there. If you have more than one, there should be a dropdown list under Authorizations. Highlight the number and copy, or write down the number. Now when you open the stand-alone version the Authorization Manager will open to authorize. I don't know why but the authorization does not work for me if I try to do it in the VST in Sonar. It only sticks when I do it with the stand-alone only. Follow instructions to the window that prompts for your number. Fill in the blank and click. If you have an internet connection it will respond that you are authorized. Then proceed to do your setup of Amplitube 3 in the stand-alone version.
As for working in Sonar, you should have a dll file in the Cakewalk VST folders of both the 32 and 64 bit versions. Check there to make sure they are there. If you have some older 32 bit VST files in your system the 32 bit dll may have been placed in the Stienberg folder for Vsts. I have had that happen before.
I know some of you are gonna say you do not need all that detail. I apologize, but this authorization for Amp 3 has run me through the hoops every once and a while. I just thought it might help clarify a little more for those that come after us.

BTW, there is no difference in the full Amp 3 and the Custom Shop version. The Custom Shop version just allows you to try and buy ONLY the amps you want to have instead of loading you down with a hundred amps that you only use 4 or 5 of.
 

Is there any way of forcing the Authorisation Manager to open? It doesn't do it automatically (I did install it)

Also the dll file saved to a folder just called VstPlugins, but I've moved it to the cakewalk VST folder... and I still have the same issue, apparently it has not installed correctly when I double click on it after putting it in the effects bin
 

Yes, the Authorization Manager should launch automatically when you first launch the stand-alone version of Amplitube 3. It sounds like the download may have been corrupt. If it were me I would probably uninstall and clean out the registry of any traces of the Amplitube 3 installation. Redownload and follow the instructions above. Make sure you use administrator when you install this time. Make sure to pay attention to where the dlls go. 

Ok, thanks!