If I was building a Meggy jr Rgb and I flipped a resistor's color order around (ex red blue gold orange would be orange gold blue red )would the device still work?

Resistors can be oriented either way, and will still work. However, if you re-arrange the color bands, you're changing the value.

Gold bands are nearly always found on the ends, not in the middle-- are these some strange-value resistors that you've obtained?