When using a dynamic model with prescribed displacements on the bottom boundary in combination with a bottom layer with Rayleigh damping results might become incorrect. Due to an issue in the kernel, part of the (Rayleigh) damping in the bottom layer may be ignored.
This issue is solved in the 2D2012.00 and following releases.
When working with an older Plaxis version you may create/add a relative thin and stiff Linear Elastic (LE) base layer without Rayleigh damping at the bottom of your model. The LE layer will simply “shift” the input time-history signal from the bottom to the top of the LE layer without affecting it, but this way the (Rayleigh) damping in the layers above the Linear Elastic layer will be taken into account correctly.