OS

i was wondering if i would be better using my windows 7 box or one of my kubuntu linux boxes to drive my reprap with.?

Linux is always better.

On a more serious note, I haven't used windows for years and years, but I hear the reprap software, skienforge, replicatorG, arduino compile etc. works fine under windows. So in theory there's really nothing much to choose between them, and you should pick whatever you're most comfortable using.

Asking such a question is somewhat akin to "which is better, vim or emacs?" it's what is refered to as a "bikeshed" problem.

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I'm building it with Baling Wire

I would strongly recommend replicatorG over the reprap software. For me it "just works" on OSX, windows and linux. On the other hand getting the reprap software to run on anything is a huge headache though windows seemed the easiest, it still crashes relentlessly.

There seems to be some further issues with the libraries for the reprap software and 64-bit anything also.

who makes the replicatorG software then. thought i would have thought the reprap people would have been trying to get that end together has well, OSS is great but even it needs to work

Not sure the exact lineage, currently maintained by some of the makerbot folks (adam) though (open source also). I should have a patch for their firmware pretty soon to support stepper driven extruders (mendel) rather than dc motors (cupcake).

the makerbot firmware does support stepper driven extruders. once you have the machine extruder setting set for it. the one thing right now that the makerbot code does not appear to support correctly is multiextruder functionality. but there are only a few of us that are agressivly pursuing that functionality.
Hopefuly soon even that will be supported out of the box. Also the makerbot code supports the use of the sd card printing features which from what ive seen from the mendel code reprap doesnt yet.

Have you actually printed with a stepper extruder? I am curious how, looking at the code there were at least 1 or 2 bugs in 1.8 that seem to me to make impossible to work correctly?

What pins/connections are you using for your stepper motor if you do have it working, maybe that is what I am misunderstanding?