Are they hanging scales, or do you put the bike on top? If it's bike on top, the reason it's different is almost certainly because you're supporting the bike. If it's hanging scales, as long as the bike's static and not touching anything the scales can't read anything but the weight, unless they just have a big error factor.
If you are using something like bathroom scales, your problem is corner loading errors (and it living in an environment that can be cold or hot and humid). You can reduce this by placing on a hard, perfecly level surface and taking a reading, then turning the scales 90 degrees and taking another reading. Repeat 3x and take the average. Even so the error margin on bathroom scales is pretty big and only gets wider the older they are. Mine were ~2lb out when I used "the me and my bike method" and ~1lb out when I rested the back wheel on and just kept it upright (blatently not a linear scale anymore). The actual weight (on E2 class industrial dispensing scales was 14.503Kg (or half an ounce under 32lb for a burlyish hardtail).
hanging scales are funny onions – I don't trust them as a rule, they are very sensitive to both local gravity and the quality of the materials they are made of, although good digital scales reduce these problems as a lot can self calibrate and have less moving bits inside..
Just because a balance says 50lb in 1 ounce measurements, don't think it is accurate to 1 ounce, it'll more likly to have a tolerence of 8 ounces.