Arduino DUE vs Arduino Uno data logging speed

What sampling rate do you need from the arduino? The UNO can acquire a few sensors outputs at a rate of at least tens of samples per second. To be able to assess the source of the problem, try to write a small program with PROCESSING on PC or using another UNO. This program will just receive the sensors outputs and print them out on the serial monitor. If the results are OK the problem is probably within the processing software on the PC. Good luck