Ill give you a little run down on whats happening.
So first off scene scale is not in fact an issue what is the issue is simulation settings. @vicnorman you were on track with Gravity. whats happening is the particles are moving to fast due to the scene scale and the Gravity.
If they move in steps greater than the SPH radius the simulation wont work. so things to look at are gravity speed and substeps lets have a look.
Here's a scene with a real world sized glass and particle radius of .1 as you can see its not working as you expect it too.
So lets change the gravity strength right down to 100.
We get this much better already.
Now we want to make it fill up more so lets do a couple of things.
First increasing the particle radius will help fill a glass more. However that will make the solver more explosive so to combat that in the FluidFX object enable "Check Density"
So in this scene we set the radius up to .4
And this is the result.
One more thing to try out you may not need it is to increase the scene substeps in this iv increased it to 3.
The result is a little more realistic.
As you can see much closer to what you expect and still using the real world scene scales.
Hope that helps.