I am analysing pipe flow (closed at tip, open at bottom), fluid is water ( laminar, incompressible) diameter of pipe is 3.1mm length 392mm. Pressure inlets - 2 eye's staggered from the pipe tip on opposing sides.

Second eye(furthest down the tip) is scaled 1.1 times the size of top eyelet.

Top eyelet inlet pressure of 2971 pa ( 10 mm from closed end at tip of pipe) Second eyelet inlet pressure of 3079.8495

distance of 5 mm between inlets

Fluid does not enter through the top eyelet, 99% through bottom eyelet. High Static pressure in area around tip to just above second inlet. What is causing this??

did you set the operating density to zero?

no density taken as defaults for water...

I think the hyrostatic head of the water may be causing the error in your simulation. You should less the hydrostatic head from your pressure inputs or set the Operating Density to zero. Have a look at hydrostatic head in the Fluent help files.