(I replied but accidentally deleted the message trying to repost it, doh!)
I can't recreate the problem on my end with a .05 step and a .06 depth of cut, I'm going to need some exact details in order to recreate the problem. What dimensions does the project have that you're working with? In case there is any confusion the 'Cut Depth' parameter specifies the depth each individual cut pass will be while the project's actual Z depth (or Max Depth, whichever is smaller) will be the total depth all of the cut passes will result in. If you have a very deep project I can imagine a computer running out of memory while trying to generate a toolpath with many cut passes, potentially hanging the program. I'll write a note to add some code for detecting if this is what is happening and pop up a notice for the user, but my instincts tell me you may be having a different problem.
I replied to Bill above with an image showing that a 50 thou step over and 60 thou depth of cut are perfectly fine for PixelCNC, at least on my end. If you could give me exact details and perhaps your system specs (CPU make/model/speed, system RAM, GPU) we should be able to figure it out and get things working for you. Thanks for trying PixelCNC!