What bearings were replaced??? You said in your 1st post ALL bearings...then asked about the carrier bearings..so did you have ALL of them replaces, axle, carrier and pinion? As was said, if the pinion bearing was replaced , the preload could be off probably off and yes when tarved for oil, the pinion is usually the 1st to go bad as said because it is the lowest in the case. The semi floating axle bearings are pressed on the axle..they also need to be "set? in the proper spot or will make noise.
You had the noise after the flush...then had the bearings replaced...you could be hearing what sounds like the same noise, but it might not be. Messing with bearings is a scince in its self as far as preloads and proper setup....so you could be hearing a totally new noise...and as i said, bearing noise "travels"....
Flushing the diff (which as said there is no reason to do unless it is contaminated) wouldn't cause a noise..the new lube might be "thinner" (in viscosity) or as Paul said, there may have been an additive in it and you just didn't hear it to begin with, but 90 weight gear oil is hard to thin out and wear out...and ive never heard of it "wearing" out, hence no need to "flush" it....unless you have had a leak over time and ran it low..then you will over heat it, thin it out and the bearings wll over heat, but a good rear axle mechanic will see the signs of a over heated bearing and wouldn't tell you very thing looks good....
Getting a 2nd opinion is a good idea, but personally, id continue to drive it and pay real close attention to the noise and look for any changes in pitch and volume...if it gets worse, you will find where it is coming from...and with bearing noise, sometimes that the only way to find it....
If you want to get over listening to the noise, come ride with me for a week...the rear tires on the Cargo Max (Bridgestone open off road thread and hard compound) are so noisy that I thought the whole rear axle was bad....Talked to a canadian that has a Cargo Max, he said the same thing....Ill will run them though the winter and they will be replaced in the spring ...After listing to this noise for a week, you won't even notice a low whine in the rear end...