This is noticeable in Dolynick's stargate mod as well: the spacegates and starbase upgrade used by the Ancients in it work everywhere except stars. The strange exception is the capital ability to create a temporary phase stabalizer does work.
The mod uses the passive stabalizer ability the Vasari gate structures have for both the spacegate and its starbase upgrade.
On page 28 of the mod thread from Dolynick, reply 683:
I know for a fact that I built a stargate at a star the other day using the Ancients and their Munio cruiser. It popped out just fine in the star's gravity well. Now, stargates (or any phase stabilizer - seems to be a game engine thing) won't work on a star it seems but the structure did build.