You can reserve seats on Intercontinental flights in Y and J and Europe Select 90 days before departure.

I found out the other day from an informed Lounge D at SPL the other reason why certain seats can no longer be booked in advance:

1) the pay-for-emergency-exit row-seats project as discussed here before

2) KL's change to Amadeus. Apparently the rows 1,9,11d/e and 77 that we all loved on the 747 were always labeled "conditionally issued" seats. KL's reservation system used to inform the travel agent upon reservation that KL could take these seats back for operational/medical reasons. That has not yet been arranged with Amadeus hence they are only available upon checkin (provided that they have not been blocked or already taken by others).
Not sure how other airlines do this, surely KL is not unique in this?
Anyway, she said that communication has only recently been given about this and that hopefully it will be fixed.
A very nice LD by the way!