I had one letter written by just a post-doc and NOT signed by a PI (it was an old lab and I barely talked to the PI), and one letter written by a post-doc and co-signed by a PI. For the latter, I listed the PI on AMCAS. Either way, it didn't seem to matter in the least for my application. All of my interviewers commented positively on my letters and nobody cared about the signature/AMCAS. At the end of the day adcoms/interviewers read the letters and see who signed/wrote them for themselves. The letter entry feature on AMCAS is more of an accountability thing.
Although I know that you have both signatures, I will add that certainly nobody asked me why the first PI did not sign my letter. A good letter is a good letter, no matter who wrote it (although high-powered letters from famous PIs do help in some situations).