There seems to be a bug in how the starbase hull repair module is counted in the newest release of Twilight (1.95).  I am unable to install the repair module in a damaged starbase even though I have the prerequisite technology and was able to use it normally while I still had battle stations mk II left to add.  Once the starbase is fully upgraded, I just get a message saying that the starbase cannot be upgraded because there are no new modules available.  Researching a technology that grants a new starbase module restores my ability to add the repair module.