I did multiple administrations of the IAT per subject. 4 to be exact. I was trying to see if I could get more accurate results after multiple trials. I also used within-subject and between-subject counterbalancing. For example, Subject 1 did 4 trials; order 1, order 2, order 1, order 2. Subject 2 did 4 trials; order 2, order1, order2, order 1. to get around the automatic counterbalancing of Inquisit. I labeled subject 1-order 1, 101, subject 1-order2, 102, subject 2-order2, 202, subject2-order1, 201. This way I maintained an entire counterbalanced sample based on the order of the subjects' initial IAT as well as counterbalancing within to see if there was difference within or if i could get a mean or aggregate score that is more representative of each subject.

Anyway, I recently tried to use SPSS syntax for my IAT data. The problem i encountered is I am not sure what SPSS did with the multiple administrations because there each subject number, eg 101, which should have two scores, only has one score. I'm wondering if there is a way to change the syntax to reflect the multiple administrations, or like i have though, have to relabel my subjects to reflect each individual trial in some sane way.

You could (a) compute the results for each IAT separately and later merge the summary files in SPSS or (b) introduce another variable to specify the different IATs and /break on that. As for how the SPSS syntax works, you could generate a set of sample data and step through the execution while at the same time studying the syntax. For general guidance on using SPSS, reading and writing SPSS syntax, I recommend you consult the SPSS manuals as well as other SPSS-specific support resources (books, courses, tutorials, etc.).