long delay needed to start opengl programme

Hi All,
I’ll try to describe this best I can. Basically I need my code to self run at boot time. I do this by using gnome sessions to start my code at start up (I’ve also used a start up script with the same effect) . What I’ve found when I do this, is my software after some time starts to run slow. The amount of time needed for the “slo-mo” is dependent on the size of my hard drive, the smaller the hard drive the quicker the slo-mo begins. The only way I’ve found to stop this is to put a 1.30-2 min pause before my software begins. I’ve checked gnome sessions and my code is the last thing to start, it does seem that something else starting after my code is causing the loss of speed but I can’t find anything. Can anyone offer any advice on this? I’m running xorg and with gnome-core, a full gnome install makes no difference.
Thanks in advance.