Because the Crown Estate has no responsibility to maintain the palaces.
It's difficult for many (including myself) to understand the concept of "ownership" by a rather obscure entity known as "The Crown" - which is neither the Nation, nor the Government, nor the Queen herself. But that's who owns it all - the Crown Estate, the Royal Palaces (occupied and historic) the Crown Jewels, and all the various other trappings associated with the monarchy - all owned by the Crown.
What people (like me) really seem to want to understand is - if the monarchy ended, who would then own these assets? It would be complicated, but in the end I have no doubt the nation would own virtually all of it. But not today! So, the real queston at hand is who "holds" or is "responsible" for each of these assets. And that gets complicated because it has evolved differently for different assets, at different times.
The Crown Estate Commissioners are today responsible for maintaining Windsor Great Park and Home Park, but not the Castle itself.
For Buckingham Palace, Windsor Castle, St. James Palace, and part of Kensington Palace, the Crown owns all of them but the Government is responsible for funding their maintenance - they agreed to pay for that when George III surrendered the Crown's right to the Crown Estate revenues to the Government.
Hampton Court, Tower of London, the rest of KP, Kew Palace, even the Palace of Westminster are all still owned by the Crown. Except for Westminster (which is managed by Parliamentary officials), the rest are "managed" by a separate entity called Historic Royal Palaces.