When I load up flight sim it starts out very smooth but after about 5 minutes it becomes a stuttering mess.  I am using the usual tweaks, any ideas why it starts fine but degrades over time?

What addons are you using? Something like the CS757 will cause a lot of stuttering when you engage autopilot. Also, are you using the Bufferpools tweak?

Update:  Ive  tried with a default fsx.cfg and a modded one using bojote's tool using poolsize=0.  Ive noticed the fps drop is related to gpu usage.  The gpu load starts around 45% but climbs to 99% after several minutes, once the gpu load hits its high the stuttering starts.

Try without the poolsize tweak. I also had severe stuttering with that tweak. Once I removed it, my framerate went up a bit and the stuttering stopped.

The 16th May 'How to' guide covers Bufffer Pools,
 
you can download it from here:-

http://www.nzfsim.org/index.php?dsp=downloads&f_sort=fixer

Ok thanks I tried with a new flight without bufferpools and no stuttering, but if I load the saved flight I was using when I first had the problem the stuttering returns.  The saved flight is using the same conditions and location.  Does a saved flight use an old cfg somehow?