Custom package in EagleCAD not aligning to grid
If the pads you are placing are off the grid when they are supposed to be on the grid, you can select the pad using the Info button and type the desired X and Y coordinates manually.

If you have lots of pads that are all mis-aligned by the same amount, there's a trick you can do using the grid. Say, for example, all of the pads are off by 0.015 inches. Change the grid spacing to 0.015 inches, select all of the pads using the Group tool, select the Move tool, right-click and select "Move Group", and slide all of the parts over by one grid spacing. Then change your grid spacing back to whatever you had before.