Hi Melanie,
Yes, both rasters are in the same projection/cell size as they have been extracted from the same raster. I had a go at changing the axis, and even thought axis=0 is correct, changing it to 1 made me realise that the raster extents are the problem. For some reason, the extract by mask tool did not update the raster extents and the original extents are still being used.
While I can fix this, I'm now wondering if the NoData cells are going to cause a problem with the alignment of the extracted rasters.
Update: seems like I'm also blocked by the differences in array dimension for each raster.