I'm not sure when or why the sign was changed, but you can spot many differences. Mainly that now the characters are not only floating heads in the distance, but closer up half-body poses. The Maroon Studios logo curves on top of them, and the names are bigger and easier to read. The background also seems to have been fixed up.
Most of the other Roger Rabbit-themed items were changed, taken down, or relocated, however, the newer Maroon Studios sign still stands in what's now knows as Disney's Hollywood Studios.