JVC RS40 and Onkyo NR5008 communication failure?

I just set up new RS40 and found what seems to be a set of communication problems between devices...

Setup:
3D: Sony BR 3D player -> Onkyo NR5008 ->(RS40 & Sumsung 2D TV)
2D: All components -> iScan VP50Pro -> Onkyo NR5008 ->(RS40 & Sumsung 2D TV)

Problem 1:
Sony BR player does not recognize 3D display when signal passes through NR5008. It says smth like "No 3D display was detected. Go buy one first". 3D works well when I connect Sony player directly to RS40

Problem 2:
RS40 does not recornize video input (it shows blue screen and weird resolution, e.g. 0x370 or so), when 2D signal from VP50pro passes through NR5008. When I connect VP50Pro directly to JVC projector everything works well. In contrast, Sumsung TV works well in all cases.

I tried sifferent settings in NR5008 (e.g., "through" resolution, etc), nothing work. I also factory reset both NR5008 and VP50Pro that did not help.

Any ideas? Thanks.

I possibly solved the 2d problem by selecting "skip" for Nr5008 that is supposed to remove any video processing. However, 3D still does not work. I have updated firmware....