The way I've understood pcolor (which I assume pcolorm is a modification of) makes a colour-patch with corners at [x(n,m),y(n,m)],[x(n+1,m),y(n+1,m)],[x(n+1,m),y(n+1,m+1)] and [x(n,m+1),y(n,m+1)], using the intensity/color from Z(n,m) (this is using shading 'flat'). Sometimes that is an OK behaviour. However when I have some small-sized data that I considere centred at the coordinate-points I have to adjust the input to pcolor to take into account the function's behaviour by repeating the last row and column of the data and modify the [x,y] coordinates by shifting a "half dx and a half dy" and add a last column and row to both. Maybe that's part of your missing-data problem?
HTH
