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Just noticed that in the current plugin (my version 3.0.995) that rendered poly-selections are not corresponding to opengl/C4D IF one of the lower selections (to the left) also contain the poly's belonging to a higher selection (to the right).

Thanks, I reproduced what I think you're referring to. If you want to work around it, the way of doing so should be to make sure that a given selection tag sits directly to the left of the texture tags that use it, rather than having all the selection tags, followed by all of the texture tags, or somesuch.

selection tag sits directly to the left of the texture tags that use it

Ah thats why it doesnt always happen, I couldn't reproduce it today, and wondered why.

Also in the latest public beta version of the C4D plugin, the bug seems to persist. I could not do any emitter with selection tags in R16, or is there a workaround?
I know that I can cut away the selection as a new object, but maybe the here mentioned problems with selections and this one with emitters are related.

The problem there will be that Maxwell does not support emitter materials being used at the sub-object (i.e. assigned to individual triangles) level.

Ok, thanks. In this case, I will use the workflow of disconnecting the selected polygons for emitters in future.