Thanks so much for coming back to me and, yes, it happens while using Map Viewer.
Your hunch is correct. The developers site you linked to has a list of Known Limitations including: There is no current support for printing highlighted features.
This prompted me to turn off the Bloom Effect within all five layers and now the layers export every time perfectly aligned to the underlying map.
And as further confirmation, if I turn the Bloom Effect on within one of the five layers, it alone misaligns, while the other four (with Bloom turned off) remain aligned.
I'm very pleased to have cracked that problem - with your kind help!