Yep, the 12" radius would be flatter-looking than 9.5" would be, so it's a good bet your previous bass had a tighter radius than this new one.
Because radius is set both from the curve of the fretboard and the saddle placement at the bridge, it affects the position of the strings in relation to each other all the way from the nut to the bridge. So, if you're reaching for the G string from the A string, it's likely to be a hair out of position (slightly higher, in this case) from where you are normally used to finding it. It may not seem like a visible difference, but to your muscle memory it could be a big deal. Did you change the saddle heights individually, or just the truss rod? Ideally, the saddle heights are set by a luthier individually using a radius gauge in order to match the radius of the fingerboard. Changing the heights individually without a gauge can also throw you off.
Anyway, this may not be the issue, but it's something to consider. It took some work getting used to my Sire (which is a P7 with a 9.5" radius) after playing my Fender, which is something like 11.5". That's why I thought of it.