typically they should be running about the same RPM. The usual culpris to check are both clean out ports feel the shafts, and if you can, reach down to the grates at the bottom of the boat and see if anything is hanging on down there that may be causing a bit of cavitation. In August, we get a lot of milfoil in our marina and it's not uncommon for some pieces to float up under the boat as it's sitting int he slip, then once power is applied, the impellers will suck it through and spit it out the jet stream. Once I'm out in the lake, I always stop, reach down to the base of the inlet, and ALWAYS get more milfoil (I then leave it in the hatch near the top of the tubes to try and keep that crap out of the main part of the lake). While you have your hand in there, reach around the impeller blades and make sure they are smooth and clean as well
The next things to check would be spark plugs, an adjustment on your throttle linkages, and you may also try removing your air boxes and running it with he filters removed (there could be a restriction in there). with so few hours on it, I'd doubt a bad plug, but you NEVER know...it could also be a gapping issue with the plug.
As others have said, fuel, people in the boat (weight), wind and current will all affect speed. There's been several times when out on Tahoe that my speed has varied as much as 5MPH on the same run....all depending on how the wind and waves are hitting. I think the key here is to try and get them to run at the same RPM.
Typically, I don't run at wide open RPM that much as it's pretty expensive to do so (to the tune of 20gph or so). If you can't find the issue, then a trip to the dealer is in order as it's a new boat. You may want to wait on taking it in for JUST that as of now though because once you take it in they won't let it back out until it's fixed. When mine was new, I kept a 1st season "punch list" of warranty items that I took into the dealer in October and basically said look into these, and It doesn't matter how long it takes as she's going into storage for the season. The dealer appreciated that as they were slower and their techs had more time to look at my issues.