It could be just the nature of Rotosound flats.
I’ve got a set on my Warwick Thumb that are a few weeks old now, and there’s a similar thing going on. The D and G are dead in that nice flatwoundy way, but the E and A are still quite zingy. It’s a bit like having two round wounds and two flat wounds on the same bass.
I came here and did some reading up about Rotosound flats, and there have been others who’ve mentioned this unusual unbalanced way that they break in. It seems that the E and A can take an extraordinarily long time to break in, and in some cases never sound exactly like the D and G.
Here’s the odd thing though - I’ve noticed that despite how they strings feel and sound acoustically, in my case I can barely hear the difference between the E/A and D/G when amplified or recorded. They sound very balanced when I listen back to recordings of this bass, despite feeling so different. There’s also that super distinctive rich midrange and low mid punch that the Rotosound flats are known for, which really is special.
So can’t say for sure, but it’s possible this is by design?!