This is a known problem with compatible cartridges for the PIXMAs and affects both the the PG-40 and CL-41 cartridges.
To get the printer to work again press and hold the Stop/Reset button (bottom right hand side of printer) for at least 5 seconds until the display reads '1' again. This will bypass the ink level detector. Until there is a reliable reseter for PIXMA cartridges you'll have to give up on ink level detection and plan to have some spare cartridges handy.
This process is also explained in the troubleshooting section of the on-screen manual supplied on the printer installation CD.