'Must be running in full OS' issue when distributing software through TS

Recently I've come up against a problem where during a task sequence certain packages do not run. I'm met with the following lines in the smsts log:

[The step (Install "2D Design-Install 2D Design") must be running in full OS]

and

[Failed to run the action: Install "2D Design-Install 2D Design". The request is not supported. (Error: 80070032; Source: Windows)]

The packages run fine locally after the ts has completed. They are silent EXE files and have been successfully deployed elsewhere in my environment however after creating a 'thin' OS image and having all programs like flash, java etc... install via command line through a TS rather than being built into the image, these EXE packages we deal with have stopped working.

All other packages including microsoft office xp / 2007 all install fine without any errors or failures. The sccm client is also succesfully installed prior to the installation of the packages.

I'm using SCCM R2 SP2.

I've added two custom 'restart PC' steps to make sure it's not a system restart that is needed.

If anyone has any ideas i'd be most greatful.

Chris