From Carrara basics and Wings to Lightwave and Maya Complete, virtually every 3D program, no matter the cost, has problems with booleans. The reason, I'm told, is that they are all "Surface modelers". Do enough booleans on the same object and something will start going crazy after a while. Form-Z is the exception, it is a "solids modeler" and I watched the Form-Z guys demo their program at Siggraph as it not only did mega booleans and not break a sweat but they actually could go back and move booleaned areas later on. I talked briefly with one of their programmers later and he told that it was because Form-Z worked with solids.