Hi,
Hope the reply is not too late. I've just noticed this thread and thought it worth commenting as you had not received an answer yet.
I've not used FLAC for consolidation analysis; but I think I can see your problem based on my experience looking at other types of analysis in FLAC. I think the initial command is not the correct command for what you need.
The way I use the initial command is to set properties to a starting condition, before stepping through the analysis. For example I use it for displacement controlled analysis to set the object being displaced (e.g. a foundation) to the same velocity as a displacement controlled boundary conditions. For a displacement controlled foundation this reduce inertial noise as the analysis does not have to jump from a zero velocity initial condition in the first few steps in the calculation. This lets me use a faster displacement velocity to reduce analysis time as well as producing cleaner data. I think the information set by initial is cleared after the first steps of the calculation so is no use for your case.
You need to find the alternative command to adjust pore pressure. However, keep in mind you may not be able to assign pore pressure over the zone in the way you suggest. You might have to assign appropriate boundary conditions then step the model to the point when it is stable. This would need to be done before apply other conditions such as a foundation load.
Taking a quick look at FLAC the command you may need is interior pp. But I've not used this before so you will need to check this out thoroughly. Alternatively assign boundary conditions using apply in the GUI.
I think there are some examples in the FLAC manuals so it's worth having a bit of a wade through these to see the approach used here.
I'm surprised your pore pressure is uniform in y, i.e. depth, surely pore pressure increases with depth below water table. If the variation in x is genuine, e.g. an uphill source or sloping site, then you may need to play around with one of the boundaries or introduce a point source, step to stability then check the conditions.
Hope this helps. Let me know if you work it out.