I'd always shot split fingers and what I considered to be a "true instinctive" shooter, i.e., not useing any conscious aiming references. A while back I swith to 3 under useing Rick Welch's principals from his DVD's, and must say that my accuracy has improved noticably.
I think it is attributed from a more consistant / smoother release than anything else.
In reference to your question, I don't think your situation is unusual, I think it is just a matter of your brain and muscle memory getting in sync with something new. If you are consistant with your form, things should only get better.
Just my $.02. but others MMV.
Best of luck.
YB