Are you sure you've gotten them set up correctly? There are a fair number of components to them:
In the pof file for the rotating subobject, you need to add something like this to the properties:
$special=subsystem
$name=Solar Panel
$rotate=5.1
Then you need to define the "Movement type" as Rotate and then pick the axis around which it rotates (assuming you set that up correctly before conversion - if not you'll have to reconvert).
In the ships table you need to put a line designating the subsystem, like this:
$Subsystem: science01a-solar1, 8, 0.0
Note that it's labeling the name of the solar panel subobject and NOT the "Solar Panel" name defined in the subobject properties.
Do all that and it will work - there's nothing wrong with PCS2 there.
