I have various tools on my USB drive and have renamed the "Start" application to "PortableApps" but every time the platform updates it creates a new "start" application in the root of the USB. Is there any way of stopping this and simply start the program using my "PortableApps" shortcut.
At present, no. It's expecting it to be one thing and just extracts and overwrites the existing one. The installer doesn't know that you renamed it and what you renamed it to, since an end user could rename it to just about anything.
Some time ago we used to use StartPortableApps.exe. I might consider writing some custom code to support that instead for users that want it to say what it does more. Supporting arbitrary renaming would be messier.
Sometimes, the impossible can become possible, if you're awesome!