I have a similar issue with MR v 12 -> AX 2012 R3 CU8. A pair of account balances are missing in MR. I can see the transactions in AX trial balance and everything seems ok. There are not errors in the integration log. I already have tried:
restart MR services (both)
restart SQL/Aos
rebuild MR datamart (disable and remove integration, stop services, delete datamart, re-configure, restart services)
I am getting crazy with this. What can be wrong?
Please help!