I have had problems reported when using xia2 to process data from the new Pilatus instrument on ESRF ID29. It seems that there are two problems - reading the image headers for xia2 and Mosflm handling the different image header that they are using. The former I have managed to mend and a patch is available, and Harry is looking to fix the latter in the forthcoming Mosflm release.
Meantimes, with the above patch xia2 -3dii or xia2 -indexer xds -integrater xdsr -scaler xdsr will work.