Without screenshots, I can only guess.
1: your structure. "a glass substrate with dimensions of 420 nm in both length and width". substrate is cosidered infinite in the periodic directions, thus, it should be larger enough and be outside of the periodic BCs. Did you use periodic Bs in yz? and the substrate larger than periodicity in yz?
2: It seems you only need one wavelength, did you use a pulse or a cw source? if you want the frequency domain result, please use the pulse source. You can use a relatively narrow bandwidth but the pulse will be long. You can use a pulse centered at the single wavelength, and set the monitor to record only this wavelength. To avoid possible issue, you can also have a second monitor to record broadband, and see the spectrum is smooth, and this wavelengh has resoance or not. it can give you some hints, for example if the simulation time is long enough.
3: for the geometric phase, since the polarization will change, maybe you can simply monitor the EyEz phase change (and their magnitudes) and do some post processing.
As a general tip in the forum, an image is worth more.