Just re-read Traymat's reference to KLM not permitting online check-in with children
I think that this restriction applies only to under-twos with a lap belt and no assigned seat. A candid employee once told me that this is just because of a software bug that they can't or won't fix. Computers can do anything but someone has to want to pay for it.
But to answer the original question, be early at the check in and if that doesn't work change airline.