Well, after my first flush of 3D printing glory, I had a “compulsory sabbatical”, due to a requirement to travel away from my machine for work purposes. (Oh, the separation anguish!) The enforced parting gave me the opportunity to stop playing and start thinking – how could I improve the design of my machine (which I only just got working, after a fashion), examining the Sprinter / Pronterface / Skeinforge settings, and so on.

In particular, I had one of those “light bulb” moments that sometimes happen when you take the time to step away from a problem, and see it from a new perspective - I worked out how to correct the non-perpendicular alignment of my X and Y axes. http://julianh72.blogspot.com/2011/08/main-frame-build-and-alignment.html

Due to the initial mis-alignment of my whole frame, for my initial prints, squares were not quite square. I had calibrated the X and Y motors so that the sides were equal in length (and correct length, as well), but the corner angles were a couple of degrees off a right angle (as I always feared). This probably doesn't matter for "sculptural" type print jobs, but for dimensionally-critical machine parts, I wanted to get everything all squared away.

Then I realised that all I need to do is move the ends of the Y-axis smooth rods across slightly at either the front or rear threaded rod until they are truly perpendicular to the X-axis smooth rods (just a couple of mm at one end was all it needed). Once I had seen the machine in action, I realised that all you need to do is get all your smooth rods for the X, Y and Z-axes mutually perpendicular to each other - it actually doesn't matter if the rest of the frame is a bit skew, as the long as the smooth rods are all square to each other.

Five minutes work with a spanner shifting the Y-axis smooth rods a bit and voila! – nice square prints!

I now realise that the design of the Mendel Prusa is actually quite clever in that each of the axis smooth rods can be independently aligned so as to be truly perpendicular to the other two axes. I am sure this is by design, not just an accident, and it is probably obvious in hindsight, but it took me this long to realise!