"Link failed" is a bit vague, particularly if said by somebody designing a network interface.
Are you talking about physical link failure, or some problem on the network layers? What do you see at the management interface? Do the negotiated interface parameters change? What's signalled by the switch (e.g. speed)?
My first guess would be inconsistent PHY parameters, respectively parameters not supported by your actual interface, possibly some default PHY settings after power-on.
It could be also a signal integrety problem of your board, resulting in unrealiable 1 GBit links.