unburrow works as intended. so does prey seeker. I just tested it.
you either are lying and didn't time it perfectly, some other spell popped the shield, or you're lagging. Reksai can easily prey seeker into unburrow, since prey seeker's faster it will always pop shield first, making it an easy knock up. she can easily be kited out of burrow form; your sivir... you have like 9000 MS. why are you complaining?
Also the knockup cooldown (that circle indicator) doesn't happen if sivir spell shields so reksai's free to knock her up on the second unburrow. (this is a bug)
Also why would you intentionally shield her prey seeker? unless they're AP reksai?