OK so i know its not really the software acting strange, but im at a loss to get my head around how it should be implimented best to avoid this situation.
I have setup a GPO so that all users of my accounts group get there start menu redirected to a network share containing a set of program shortcuts.
I noticed in the eventlog of the TS that it was generating errors about re-directing the folders "programs" and "startup" so i checked my network startmenu and sure enough there was no folders there with these names, i created them and the errors went away.
To avoid confusing my users with having a list of shortcuts on the start menu and a folder called programs i figured at this point i can put all my shortcuts in the programs folder.
However after doing that they still show up in they start menu here is a pic to help clear up any confusion.

The startup folder is also located within the programs folder.
What am i doing wrong ? or how do i go about doing this the correct way??