It happens on all subjects. I have noticed now, that when I ran it on a subject that I have never had run it on before I get this output:

MASK LIST:
Adding DLPFC_-40_46_24_HC_gr_PAT_neural_LA_mask.nii to mask list
Log File: BGG_3032_PPPI_12_8_2014.log

PPPI Version: 13.1.4-17-2014
Parameters used:
Processing subject: BGG_3032
VOI file : F:\AG_Diplomarbeit\Preprocessed_on_Windows_Machine_swuaf_VBM8\batch_templates\SS_gPPI\VOIs\DLPFC_-40_46_24_HC_gr_PAT_neural_LA_mask.nii
Output file will be: BGG_3032_DLPFC_-40_46_24_HC_gr_PAT_neural_LA_mask_cond_session#_cond_PPI_regressors.txt
Valid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Valid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Valid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Valid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
ESS image 10 : ...written ess_0010.img
spm{F} image 10 : ...written spmF_0010.img
Contrast : Omnibus F-test for PPI Analyses
Analysis : Psychophysiological Interactions
Extraction : eigenvariate
Tasks : _0_Task_on
Method : Condition Specific
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Volume of Interest'
## Note: this VOI facility is in a beta version. ##
## Interface and features might change in the future. ##
VOI saved as ..-40_46_24_HC_gr_PAT_neural_LA_mask_BGG_3032_Sess_1.mat
Done 'Volume of Interest'
Done
VOI has 1 voxels in 3.500000e+000x3.500000e+000x3.500000e+000 space
VOI has 1 voxels in 3.500000e+000x3.500000e+000x3.500000e+000 space. This is in the the same space as the input data and functional mask.
SPM8: spm_fMRI_design (v4185) 18:31:23 - 08/12/2014
========================================================================
Saving fMRI design : ...SPM.mat saved
SPM8: spm_fmri_spm_ui (v4421) 18:31:23 - 08/12/2014
========================================================================
Mapping files : ...done
Calculating globals : ...done
Saving SPM configuration : ...SPM.mat saved
Design reporting : ...done
estimate_PPI.m
SPM8: spm_spm (v4515) 18:31:26 - 08/12/2014
========================================================================
Initialising parameters : ...done
Plane 39/39 , block 1/1 : ...done
Valid Contrast
Valid Contrast
PPI Contrasts were not estimated for some reason.

Yet if I run it again on that subject I get this:

SUBJECT LIST:
Adding BGG_3009 to subject list
Adding BGG_3031 to subject list
Adding BGG_3032 to subject list
Adding BGG_3036 to subject list
Adding BGG_3038 to subject list
Adding BGG_3039 to subject list
Adding BGG_3041 to subject list
Adding BGG_3047 to subject list
Adding BGG_3055 to subject list
Adding BGG_3057 to subject list
Adding BGG_3059 to subject list
Adding BGG_3060 to subject list

MASK LIST:
Adding DLPFC_-40_46_24_HC_gr_PAT_neural_LA_mask.nii to mask list
Log File: BGG_3032_PPPI_12_8_2014_3.log
PPPI Version: 13.1.4-17-2014
Parameters used:
Processing subject: BGG_3032
VOI file : F:\AG_Diplomarbeit\Preprocessed_on_Windows_Machine_swuaf_VBM8\batch_templates\SS_gPPI\VOIs\DLPFC_-40_46_24_HC_gr_PAT_neural_LA_mask.nii
Output file will be: BGG_3032_DLPFC_-40_46_24_HC_gr_PAT_neural_LA_mask_cond_session#_cond_PPI_regressors.txt
Contrast : Omnibus F-test for PPI Analyses
Analysis : Psychophysiological Interactions
Extraction : eigenvariate
Tasks : _0_Task_on
Method : Condition Specific
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'Volume of Interest'
## Note: this VOI facility is in a beta version. ##
## Interface and features might change in the future. ##
VOI saved as ..-40_46_24_HC_gr_PAT_neural_LA_mask_BGG_3032_Sess_1.mat
Done 'Volume of Interest'
Done
VOI has 1 voxels in 3.500000e+000x3.500000e+000x3.500000e+000 space
VOI has 1 voxels in 3.500000e+000x3.500000e+000x3.500000e+000 space. This is in the the same space as the input data and functional mask.
SPM8: spm_fMRI_design (v4185) 18:45:00 - 08/12/2014
========================================================================
Saving fMRI design : ...SPM.mat saved
SPM8: spm_fmri_spm_ui (v4421) 18:45:00 - 08/12/2014
========================================================================
Mapping files : ...done
Calculating globals : ...done
Saving SPM configuration : ...SPM.mat saved
Design reporting : ...done
estimate_PPI.m
SPM8: spm_spm (v4515) 18:45:02 - 08/12/2014
========================================================================
Initialising parameters : ...done
Plane 39/39 , block 1/1 : ...done
Valid Contrast
Valid Contrast
PPI Contrasts were not estimated for some reason.