Sorry for replying so late.
As you have guessed, you should leave the ImgBurn setting to automatic when burning from PgcEdit. The layer break sector is passed via CLI argument.
If you want to burn the same image later, w/o PgcEdit, the automatic option is also recommended. As ImgBurn inspects the IFOs, it will find the cell with the seamless flag clear, and correctly placed in the middle of the compilation and at the beginning of an ECC block, and will use that cell. If, per chance, there are several cells suitables for the layer break, ImgBurn will (probably) open his layer break selection window, where you should be able to select the same cell.
Note that PgcEdit is still able to use DVDD to burn, but in this case the procedure is different, because DVDD has no /LAYERBREAK CLI option. The LB sector is forced in the DVDD settings in the registry, before DVDD is launched.
I do not recommend to use DVDD. I will probably remove the support for DVDD later, because it is not as safe and clean as the ImgBurn support.
I have no idea why you got this jitter peak in your first attempt. It might be because you forced a wrong LB sector. BTW, the LB sector must always be a multiple of 16 (32KB.)
And thanks for the thanks!