The major problem, as I understand it, is that Kijfhoek - Barendrecht - IJsselmonde / Rotterdam harbor line is used by both the dedicated freight trains on the harbor line - Betuweroute - Germany and freight trains that use the domestic rail lines. The new Betuweroute and the upgraded harbor line have ETCS (the one on the harbor line as well as the very last part of the 25 kV electrification are about to be activated I believe) and the rest ATB-EG.
As usual (at least over here) it is a both a technical problem and a monetary one. If I understood things correctly this weekend, the technical side has not been figured out completely and the usual wrangling about who pays for what and when also has not come to a satisfactory conclusion for all parties involved. The same problem exists at Zevenaar at the other end of the Betuweroute. We had an incident there just a week earlier.
ATB-EG is the first generation train control, again as I understand it, and it has a design feature that allows limited operation when there is a system failure. The max speed then is 40 kph. This was done to keep things fluid. Which is why almost all major accidents of the last ten years or so have involved trains moving at speeds below 40 kph.
The design feature could now be regarded as a mistake or flaw I guess but it does come in as very handy on a railsystem with 5000+ passenger trains, 200+ freight trains and about 1.2 million passengers a day. Leave those passengers stranded for very long and things might go out of hand.
For a long time it was stated that ATB-EG and ATB-NG (new generation) could not work together but some time ago it was proven that it could (on the Gouda - Alphen aan den Rijn line were regular haevy trains use ATB-EG and light rail ATB-NG). So ATB-NG has been installed only in dedicated places like large branchline networks in the north and east. According to Wikipedia the last ATB-EG has been installed as recently as 2001-2002.
See this map: http://nl.wikipedia.org/wiki/ATB_Nieuwe_Generatie
red = no ATB (2 short freight only branches, 1 inactive passenger line, 4 museum operations and 3 active and 2 inactive border crossings with Germany in the southeast and 3 bordercrossings with Belgium in the south)
blue = ATB-EG
dark green = ATB-NG
light green = ECTS/ERTMS
The relevant Wikipedia articles in Dutch (for those who want to translate things for themselves):
http://nl.wikipedia.org/wiki/ATB_Nieuwe_Generatie
http://nl.wikipedia.org/wiki/ATB_Eerste_Generatie
There are also two variants:
ATBM+ which is in use on the line Den Haag Mariahoeve - Leiden - Hoofddorp (-Schiphol and Amsterdam) to allow the Thalys tgv sets to run at 160 kph were everything else is restricted to 140 kph. It overlays some ATB-NG features on ATB-EG.
ATB-E (E = eenvoudig or simplified) is a system were part of it (the brains so to speak) is in a movable box. It is used for some rail construction equipment as well as steam engines from museum operators. By law since 2009 everything that uses the tracks must have ATB.
Hope this clarifies things.
In this small, densely populated country things often take a long time to get done, particularly if it relates to spatial planning. Everyone wants to have a say in matters / wants to be heard / express an opinion. Often incidents like what happened at Barendrecht are needed to speed things up. If you ever had the pleasure of working with my countrymen and -women you know what I talk about.