OP, I've just had similar issues with a mix of BA & IB flights - its very frustrating. Not possible to check-in on IB website and app for the outbound second leg and the inbound second leg. Outbound, on-line message implied second flight had been cancelled. On the return trip on-line message was that the ticket had not been issued. All OK of course and I picked up the relevant boarding passes at the airports.

Doc Copper