the only thing I can think of is...well, 2 things...either when you selected them your tool may have been feathering a bit, or the delete after inversion failed to work. I hope you still have the file before merging. Have you tried merging "selected", or, not merge all...flatten? Oh, oh..oh...how about layer properties? Maybe you failed to put the layer property up to 100 before you merged? I am sucking air, here. I bet it is something in layer properties, though. (Hoping, for ya, anyway.)