I am also using Windows 10 and Mathematica 12.3.1. And I can not reproduce the issue. No matter how many times PlanarAngle[{0,1} -> {{-Sin ... is evaluated the output always contains Conjugate
Table[PlanarAngle[{0, 1} -> {{-Sin[\[Phi]], Cos[\[Phi]]}, {Cos[\[Phi]], Sin[\[Phi]]}}], 50]