The D3D11 p_s_50 shader model supports up to 32 registers (four 32-bit components each). I don't think you are going over the limit (in your second example), I think instead the compiler doesn't know what interpolation mode to use for the uint3[4].

From http://msdn.microsoft.com/en-us/library/windows/desktop/bb509668(v=vs.85).aspx

1. When using an int/uint type, the only valid option is nointerpolation.

I can't test anything at the moment, but perhaps prefixing the uints with nointerpolation will help?

Also, perhaps use MASKVALUEPOINTS0 for the first, and then MASKVALUEPOINTS4 for the second and MASKVALUEPOINTS8 on the third. I seem to remember hitting a similar problem once when passing an array of items to a hull or domain shader.

struct PS_PAIReduc{
    float4 Pos : SV_POSITION;
uint3 MVPa[4] : MASKVALUEPOINTS0;
uint3 MVPb[4] : MASKVALUEPOINTS4;
uint3 MVPc[4] : MASKVALUEPOINTS8;
uint Loct : LOCATION;
};