There appears to be an issue that when hold-fire railguns are moving they can fail to fire when they are lined up with their target.
This is most obvious with ships that are supposed to spin.
Consider the following ship, when it is spinning the and the railguns are on hold fire they should fire at their given target as they rotate past it. However, once the ship is rotating at a moderate speed the railguns will often not fire.

Note: By running the railguns on auto fire it is clear that shots are moving fast enough to not impact the surround armor when spinning.
I assume this issues is caused by some form of target alignment check is too infrequent to detect the alignment.