I just went through this a few weeks ago for flights on KL JFK-AMS-DXB and DXB-AMS (KL) and AMS-EWR (DL). It look 7 phone calls to get it hammered out, and between hearing the various "issues" agents mentioned on the DM line that prevented them from issuing the upgrades, combined with what I read here on FT, I finally was able to give the last agent step-by-step instructions for what I needed (and then the whole thing was done within 15 mins).

I had signed up for a subscription to EF, to start, and picked out flights that had Z class availability on KL when I booked the flights. I then called the DM line, told the agent I wanted to use my GUCs and that I found Z class availability on those flights, which I specified is what KL segments require to be upgrade-eligible. Once she confirmed the Z availability, I then said that I wanted to confirm that my DL-marketed, KL-operated segments were fare eligible (everything is except for Basic Economy, which I already knew, but then at least she could confirm for herself that I was good to go), and then then asked her to convert the segments to KL codes so that the GUCs could be applied.

She had to get the international ticketing desk (or a similar name, I can't remember the exact nomenclature) to do the reissue, but it was just some hold time at that point.

I've also had good success calling the Singapore reservations line (another tip I read about here on FT ), where for whatever reason, they seem to know the drill without needing as much hand-holding on the DM policies.

Yeah, it's more of a headache than it should be, but if you know how to work the system, you should (eventually) be able to get the GUCs to work for you.