Dear Anthony,
interpreted SPM does many things that do not work in compiled mode (like adding toolboxes and other batch-enabled tools at startup time). This is neither necessary nor allowed in compiled mode. To compile SPM, you should look at config/spm_make_standalone.m. This file contains all the information necessary to pick up all relevant paths, toolboxes etc. By default, spm_standalone.m is used as function entry point. You may want to modify this to run your script instead, or you may even be able to modify your script to run with spm_standalone.
Hope this helps,
Volkmar
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