Shivans had beams in FS1, but only Lucifer used them.
The fleet that attacked in FS1 might have been consisting of outdated versions of Shivan ships, which lacked beams.
This fleet might had been around since destruction of the Ancients, perhaps searching for surviviors (though 8000 years may seem a bit long for that, but have you ever lost a key?
).
When Terrans and Vasudans destroyed the fleet, Shivans might have thought that this was the work of Ancient surviviors (which may be partially true, considering the teories that Vasudans were descendants of the Ancients) and decided to sent the fleet that was up to date to deal with them. They might have not excepted them to develop new technology.
In ASW, Lucifer's fleet was up to date and on ordinary assignment.