Haven't had any problems getting credit to KrisFlyer account for AI flights. I put the FF number in the booking and it automatically gets credited from AI. Haven't had to do any manual claims for missing credit as yet.

Dont think it has anything to do with flight numbers except perhaps in code share situations. AI decides which flights are eligible or credits not partner airlines. In this case it would be based on the booking fare code. Not all codes are eligible.

What was the booking fare code for your ticket? Which FF number if any had you put in the booking?