I am unaware of any direct statement on the reason for this by anyone involved in Lucasfilm, but after the release of RotS, the Expanded Universe trilogy The Dark Nest was published, in which Luke finally discovers the identity of his mother due to a malfunction in R2-D2. R2-D2 had kept the knowledge that Luke's mother had died in childbirth from Luke as part of his "owner-protection protocols," which explains why the droid had not revealed Luke's true identity or that of his mother (or father, prior to TESB) during the original trilogy.
It is highly likely that George Lucas had input on this storyline; it was Lucasbooks favourite - and the favourite of no Star Wars fan ever - Troy Denning who wrote The Dark Nest Trilogy, and there is a good chance he was given that role to keep other authors and comic book writers from fighting over who got to reveal Amidala as Luke's mother in the EU. This was after the switch from Bantam Books to in-house publisher Lucasbooks in 1999; George Lucas took a far more hands-on role with the EU at this point, to its detriment.
EDIT: To add to my answer now that I'm home, the novel that contains the revelations about Luke's mother is The Swarm War. There is also a section of this in R2-D2's Wookieepedia entry:
In 35 ABY, when Luke was fixing R2-D2, the Jedi encountered a recording of his father and mother discussing a dream of Anakin's in which his mother had died in childbirth, and another recording of Padmé talking to Obi-Wan Kenobi about Anakin. The recordings, however, were apparently encoded, probably by Alderaanian technicians. R2-D2 himself refused to show Luke or Leia the recordings and insisted he was trying to protect them. The only way to remove the recordings safely was to either find the original designers of the unit, a prototype, or erase R2-D2's memory, an idea only C-3PO seemed to take seriously. Because the recordings hadn't been removed, R2-D2 began to malfunction. By 36 ABY, a year after the first recording was shown, R2-D2 seemed to be functioning again, though he remained unwilling to show the recordings. It wasn't until the Swarm War, when Luke needed to see it to help him in his fight against Lomi Plo, that R2-D2 finally revealed Padmé's death to Luke, as well as his and Leia's birth, and an image from a Hologram inside the Jedi Temple showing Vader and the 501st carrying out Operation: Knightfall at the exact moment Artoo hacked into the Jedi Temple Security system and watched Order 66 happen at the Jedi Temple on Coruscant.
Unfortunately, I still can't find a reason for this, but it would seem it was done so the cheap, cop-out reveal could be executed in The Swarm War.