Hi there,
Your project gave funny numbers at HSMC_TX_D_p[16] (0.38V) and HSMC_RX_D_p[15] (0.34V), so I decided to start it all over by launching the DE2-115 system builder and keeping HSMC as default (you still have to select HSMC Default in the drag-down column).
After making sure the jumper at HSM_VCCIO is installed on 2.5V, I then powered up the board I got 2.51V at both HSMC_TX_D_p[16] and HSMC_RX_D_p[15].
I've uploaded my project here for your reference. I understand it still doesn't explain why there's a small difference, but at least you could give it a try over there and see how it goes, given that I couldn't duplicate your result based on the project that you uploaded.
David from Terasic