Software fails after a few minutes

I use the software with a home built telecine system. An optical switch clicks the mouse for every frame of film. After a few minutes, about 4000 frames, the software seems to fail to keep up. When I stop everything, the software keeps clicking for a while, then stops before crashing. Everything captured up to that point is lost. A nine minute film had to be captured in three chunks and assembled in Final Cut Pro - I was hoping to be able to capture several hundred feet of film in a single project, 20,000 frames and up. That doesn’t seem possible at the moment.
Mac Powerbook Pro 2.3 GHz i5
iStopmotion 3
OS 10.8.5
500GB internal SD drive

What type of input device are you using?
How fast are you clicking?
Why aren’t you using the timelapse feature build into iStopMotion?