It was rather obvious with the skipping of "Destiny of the Daleks", where Romana I (Mary Tamm) regenerates into Romana II (Lala Ward - who also played Princess Astra in the previous story).

Despite the impression people had that the issue with Terry Nation's estate had been resolved, the problem with the original series seems to be that when this particular deal was made, only some of it had been sorted out, so they are stuck with it as-is. It's possible we'll also be missing out on future Dalek stories, unless they can renegotiate.

This is the official response from the ABC:

The ABC was not able to access every Doctor Who episode from BBC Worldwide and sadly 'Destiny Of The Daleks' is not available for broadcast. Our Programming Department advises that at the time we acquired the rights to repeat Doctor Who, there were legal issues surrounding the estate of Terry Nation. The negotiation of these issues that you mention, were in fact to enable the Daleks to be featured in the new series.  At this point in time the legal issues relating to the original Doctor Who series have not been resolved and are unlikely to be resolved in the near future.

The BBC was able to clear Genesis of the Daleks, although each storyline has to be cleared on a case by case basis.  It is not the ABC's intention to disappoint viewers by not broadcasting certain episodes.  Essentially we broadcast what we can get the rights to and if we don't broadcast the story it is simply because we can't get the rights.