OP - It would be interesting to know what VA status you were at the time of booking, and if you put your number in at that time or added it later.
Speaking from personal experience, and discussions on this forum, I was Gold at the time of booking MEL-SIN-HND/KIX-SIN-MEL last year, but not when I actually travelled. Gold was going to expire after I had booked, but by the time I got to HND I would requalify.
SQ systems pull through status at the time of booking - I was actually Silver when I checked in (checked in online first to make sure that the boarding pass had it), and it printed PARTNER GOLD on the boarding pass. So we used the J check-in to drop bags with no hassles, priority baggage tags, were encouraged to go to the lounge in MEL and had no problems going into the SilverKris lounge in MEL and no hassles when boarding early. Same with departing SIN (we had a few days stopover) - no hassles checking in at W check-in (still got Business Class priority bag tags), no questions at the KrisFlyer Gold lounge (not worth it, IMHO, but at least we checked it out). Technically qualified by the time we landed in Japan, so when we left Osaka, I at least felt legitimate in the knowledge that I actually was Gold in the VA system (of course, boarding passes still said PARTNER GOLD), though no SQ operated lounges in KIX.
So in sum, I'm surprised you had problems, but I wonder if you were Silver at the time of booking, hence when you made Gold, their systems didn't reflect it?