Thank you for your positive comment on BoltGen. Yes, threads that correctly match are an issue. I assume that you are using the Thread Cutter function and the nuts that are created when run. Nut threads are different than bolt threads in shape and size. I use a default value (1.12 multiplier I believe) to increase thread size for the nuts. You can change that with the thread stretcher to further increase or decrease thread width of the Thread Cutter.
Each rapid prototyping machine is slightly different as to the thickness and depth of each layer. For instance, I can make parts that have 0.007 thickness or 0.010 thickness each layer. During the extrusion process, excess material can increase the width of the layer so that the final parts are slightly wider than specified. That is why I included an X-Y stretcher for the Thread Cutter ... to allow for increasing or decreasing the thread cutter prior to making nut threads. Experimentation is necessary to determine your rapid prototyping machine's characteristics.
As a final note, I have been able to use standard thread tap and dies to clean up the plastic threads with spectacular results. They work smoothly after cleanup. Rapid prototyping machines can not make clean threads due to the horizontal layering during creation. There are always small horizontal steps in the threads. A die will clean up bolts and a tap will clean up nuts for smooth operation. Alternatively, you can experiment with different stretch values on the thread cutter to find a value that works directly with rapid prototyping without post thread cleanup.