EDDB etc. often seem to miss the availability of these 'rares' at their source station.
I suspect this is due to the artificial rationing of these commodities. A source station will only allow you to by 'so many' of the rare in a single visit, so if the personal limit is six and you have four, it will only offer two to you, whereby three other CMDRs in the station at the same time who have none on board will see six available each.
As these sites rely on us using add-ins to upload data (and possibly a fair volume of cmdr traffic to the source stations are to obtain the rare commodity), there may be an issue depending on when a PC reports data back to the database. If a player's PC reports to the database after the player has purchased a full load of the rare, the player's PC will upload zero available to the external database (whereas other commanders would see availability). I suspect this is why the 'rares' often are not shown as available on these databases.
(Added a few minutes later... Obviously sometimes the systems go into states where the 'rare' is genuinely not available, but I suspect my reason is more common for the 'zero availability' reported on community tools)