I am using the velocity inlet boundary condition to initiate flow over a flat plate, and pick up viscous boundary layer effects. I set the velocity inlet to 60 m/s in the x-direction and 0 m/s in the y-direction. After the solution converges, I get 62.3 m/s in the x-direction as the free-stream velocity above the boundary layer.

Why is fluent not holding my boundary condition? Any insights into this matter would help...

The boundary layer is actually reducing the available cross-section for the fluid to pass over the flat plate, therefore a slight acceleration is occuring, so the mass conservation could be attained. To minimise this effect, simply move the upper boundary (usually "symmetry" type) further from the plate. You will immediately notice an improvement.

All the best,

Razvan