Having had similar problems in the past you have my fullest sympathies. Took a looooong time to sort out.

1) Make sure your TA removes all reference to your Kris Flyer # from their records (from their file for you not just the individual booking). Some TA's think they're being helpful supplying both numbers in the booking but can create a lot of pain afterwards.

2) If you have status on LH then check your boarding pass says something like SQxxxxxxxx in small print and, most importantly, in larger print LH*G (or LH*S) - this shows miles being credited to LH. If it doesnt appear like this then ask check-in to change your FQTV and FQTS (remove the krisflyer number if necessary) and reissue the BP.

3) If multiple sectors then check all BPs. Sometimes check in will only change the FFP # for the first sector.

4) If book online make sure your M&M number is stored in your profile, and select this when booking.