Using MTRM 1.0.0.3, any saved recipe is rotated sideways (90°). Probably a wrong order of for loops somewhere but so far I was unable to find such loops. Maybe the initialization of the GUI is to blame?

produces

recipes.addShaped(<PneumaticCraft:printedCircuitBoard>, [[null, <ore:circuitBasic>, null], [<EnderIO:itemMaterial>, <EnderIO:itemMaterial>, <EnderIO:itemMaterial>], [null, <ore:circuitBasic>, null]]);

LOL ok, that needs to be fixed asap :p
I think it might be going wrong where it reconstructs the packet on the server side.