If the rxoutclk is not driven by the recovered clock, the software currently does not set RX_PROGDIV_CFG (it leaves it at 0.0).
If this happens the refclk output will be flatlined. To fix this, set the RX_PRODIV_CFG to the divider value you would like.
Please refer to the definition of RX_PROGDIV_CFG in the GT user guides. The RX_PROGDIV_CFG would normally be equal to the internal_datawidth but can be set to any of the valid settings outlined in the user guide.
Although the problem is fixed in the 2014.4 release, you will need to rerun the GT Wizard for the fix to take effect.
The OBUFDS_GTE3 is not involved in this problem as the signal is not toggling when it leaves the GT.