I don't think the arduino serial monitor (if that's what you referred to) was designed to take more than a moderate amount of data, but I didn't look at the source code. If you suspect the serial monitor, why don't you try something more suitable as a serial monitor, such as tera term? You should be able to enable serial logging and the monitor will handle more data better than arduino IDE. Is your program entirely on arduino or did you also program your PC? If it's entirely on arduino, try a raspberry pi as the data logger. Using a coir i5 is a huge waste.