Are the pads somehow not on the bottom? Because with a "single sided" board (which seeedstudio doesn't normally do), it doesn't matter what side the traces are on if the pads are actually double sided and through plated. The circuit is the same. If you actually only sent one copper layer file, then yeah...one side would be missing the pads.
Find somebody good and stick with them. iteadstudio has been working well for me.
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