I use PTBatcherGUI to stitch multiple panoramas in Hugin using the following the menu sequence:
File --> Search directory for... --> Images...
This then generates the .pto files that the batch processor can then use. However, the outputs are cropped and the projection varies (images are shot on a carefully levelled tripod with rotating motion only). Is there a way to force the batch processor to output uncropped images with a cylindrical projection?