I am interested to know if there is a commercially available 3D finite element package that is able to calculate the long-term deflections of post-tensioned concrete slabs.
I know that the package we use (NEiNastran) supports prestress analysis in most of the solutions and also has support for tension-only cable elements which can have different types of preload. When you say long-term deflections do you mean creep?
Have you looked at how RAM Concept does its deflection calculations.
Unless it has changed very recently, cracking is defined by the designer as a factor of gross inertia for deflections, it is not calculated based on the actual stresses at each cross-section. Long Term effects are by a factor normally used only for RC design and then a very inaccurate factor anyway even for that.
You will get your best deflection estimates for RC and PT slabs from RAPT 2D (