I have the same issue - I received a spend $50 x 2 weeks. Same as you, activated the offer (which showed on the account), completed the $50 spend for week one (which ended yesterday), congratulations on the docket etc. Second week starts today - have been travelling, and am only just home and checked my Flybuys account. The offer is now not showing under "Offers", isn't in expired offers either - will have to see what happens when I do the $50 spend this week. I've kept the emails and the docket from last week so will keep an eye on it in case I need to chase it up.
I did my Week 2 qualifying shop today and the "congratulations" message was on the bottom of the docket saying I'd collected the 4000 points, so will check my account over the next couple of days to make sure they post. Interestingly, the offer has today reappeared on my Flybuys account!