I've got a similar problem. I'm trying to price SYD-MAN, MAN-AMS and AMS-SYD in Y on the EK site.

I select the SYD-MAN (EK) flights, and MAN-AMS (only available on KL). So far so good.

When I "review" at that point - expand the + sign for the segments - all flights show as Economy. Still good.

But when I select the AMS-SYD (EK) flights, the pricing page has (a) an apology that it can't give me the requested class on all sectors, (b) the KL flight showing J, (c) a note under AMS-SYD that it's not in the requested class (but it is) and (d) a total airfare of ~$15,000. Something is really wrong.

I assume that this is a problem of EK's system accessing KL's data/pricing/??? Annoying.