Most wheels bed in over the first 500km or so. Spokes wind off, nipples seat into the carbon bed. Wheels can go slightly out of true early in their life - and it's common. Even if they don't go out of true, slacked off spokes result in a less stiff wheel.

Find a good local wheelbuilder, have him take a look and retension the whole wheel. Not just fix the slight wobble, as that doesn't address the core issue and you'll have ongoing issues. It will take him 15 minutes and cost probably $30 or less. Have him do the same on the other wheel that is still true. Have him check all tensions with a tension meter.

I've got/had Reynolds wheels that I've flogged into the ground, and they have held up admirably.