I have noticed also, that when I am using the wrapper script I am losing spm defaults:

>> spm('CheckModality')
Modality is not set: use spm('defaults','MOD'); where MOD is one of PET, FMRI, EEG.
??? Error using ==> spm at 495
Unknown Modality.

This becomes noticable when I want to display results using an spm.mat on 2nd level, for example, I cannot do it anymore. I first have to set the modality again.

spm('defaults','fMRI')

Yet when I just use PPPI(P) as a command (without wrapper), then I still get the error message 'no inmask voxels' but I don't lose the spm defaults. I don't know if this is just a symptom of the problem or part of the reason.