Hmm, total shot in the dark here but:
The Eye of araan?
"I'am forever present, and forever secret": It was present throughout the HW series, but never known.
Ships pass through me without ever hitting me": When a ship enters Hyperspace they pass through the eye's networks without knowing.
"I have been traped inside ships": The Hyperspace cores were the Key for the eye, and they were used inside the Mothership, Bentus, etc.
"I have been let loose on the Galaxy countless times": The eye was posibly active when the Progens were still around, and again when Sajuuk united the cores?
"Never seen, Never felt, Never known": The eye wasn't discoverd till sajuuk united the cores, so during HW1 and cata, ships would enter and pass through the hyperspace networks that make up the eye without ever known or feeling it.