At the top of 45b, the Gemoro is quoting a Baraisa supporting the second version of Shmuel. However, I am not clear as to the meaning of Rashi DH BaMeh Devorim Omurim, as Rashi says "... VeHaino KeLishno Kamo..." ("this goes according to the first version of Shmuel...")
Those words of Rashi belong on Amud Alef, and they refer to the first Beraisa that supports the first version (all of Rashi at the beginning of 45b until the end of DH "Ba'Meh Devarim Amurim" belong on Amud Alef). This is clear from Rashi's words there, as you point out.
Thanks, and be well!