It's been a while since I last time visited creativecow, so I didn't have a chance to notice your posts about my exporter from Blender to After Effects.
I must admit that I never had a need to export animations longer than about 30-60 seconds, so didn't encounter issues you describe.
Unfortunately I don't know how to fix this. It's simply the way After Effects scripts work. Recreating animation via script takes a lot of data, so 3000 or 6000 frames long animation may be simply too much. It all has to be put into RAM and if there's too much - it'll crash AE.
I don't think I'll be able to do anything about it. The only solution I see at the moment is to do as you do - split animation into chunks.
If you have any questions or suggestions, please contact me. (You can use contact form on my site)