Problems with batching confounds and atlases

Dear Alfonso and other Conn users,

I had previously been using conn_batch successfully. I recently amended my script as I wanted to regress out the timeseries of a specific ROI, and since then I have been having some difficulties.

atlas_files = 'pathto/rois/atlas.nii'
confound_files = 'pathto/confound_roi.nii')

batch.Setup.rois.names{1}='atlas_name'
batch.Setup.rois.files{1}=atlas_files
batch.Setup.rois.multiplelabels(1)=1 %lets conn know this is an atlas multiple roi file
batch.Setup.rois.names{2}= 'confound_roi_name'
batch.Setup.rois.files{2}=confound_files
batch.Setup.rois.multiplelabels(2)=0

batch.Denoising.filter=[0.01, 0.1];
batch.Denoising.done=1;
batch.Denoising.overwrite='Yes';
batch.Denoising.confounds.names = {'confound_roi_name'}

I now have a problem in that the atlas file only generates a single beta (previously I got a separate beta for each ROI), this is despite the fact that when I look at the project's .mat file in the conn GUI the 'atlas file' check box is checked appropriately.

If anyone is able to shed any light the issue I would be most grateful, please let me know if anymore information would be helpful.

Many thanks

Rob