Might need a little more info. Are you running components or were you referring to the rear speakers? Did you do any mods to the speakers at all? Were you getting sound out of all of them prior to swapping head units? Last but not least, if you "jiggle" the wires on the back of the HU, does this affect anything? (bad connection or badly wired plug-ins on the HU).

One thing I've done before is to take speakers & test them on an older, wired, house radio. If I can get good sound out of them there, then it's either in the wires or the HU itself. Don't rule out HU problems though. It does happen occaionally. I had one installed in 2013 that never reliably delivered a radio signal; worked fine with my MP3 player though.