Similar behavior on my a570 is caused by lack of RAM and happens earlier than yours (in image count, not time). It's due to each newly created ???CANON directory reserving space in RAM and the camera's incapability of cleaning up ones that it doesn't really need -- the firmware wasn't written with >5000 shot timelapses in mind... If you find that your timelapses seem to always crash when the camera was supposed to enter the next ???CANON directory (on the a570 that happens every 2000 shots), this is probably what's happening to you too.
The remedy is to periodically reboot (and preferably moving photos away from where the camera can find them, at least on my cam otherwise booting becomes very slow). Good news is that it's supposedly possible to automate this -- I'm assuming you are already moving the images out using the eye-fi card, but you also need to make the script autostart on reboot, and program it for periodic reboots (I guess every 10k shots would work in your case) and probably have the script configure some camera settings like zoom and focus that Canon fw forgets at shutdown.
Oh and a simple optimization is to reset the jpeg file naming counter each time you start a new timelapse -- that way the camera will be filling all directories with the full amount of 2000 photos. Also, you may wish to see what you can do about CHDK RAM usage by building a version that uses less RAM and by disabling some possibly RAM hogging CHDK features from the menus, and if you're feeling adventurous, you may want to try the exmem hack. But if you're expecting a month's worth of images or more, you'll really need to reboot every now and then no matter what.