I have written a script that runs three different experiments comparing attitudes towards obese people. When I run the program it gives me a sum (following Greenwald's IAT protocol) for each independent section. If I download the raw data and process it in SPSS, however, I get the same score for my first experiment, but for my second two experiments the score is a little bit different. Is this normal? Or do I have an error in the script that I need to hunt down?
No, it's certainly not normal. There may be tiny differences due to rounding error, so I guess it depends on what "little bit different" is actually supposed to mean.
Probably yes -- either in the Inquisit script or in the SPSS syntax.