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I just added the ability to set the rounding level of the vertex positions.  Its called 'Map Precision' and can be found by the build map button.  This should let you adjust the rounding without having to crack open the script.  I have not heard about the build button crashing the whole program, if you can capture an error or shoot me an example blend file I'd love to dig into that and find the problem.  I also just fixed a few annoying errors that seemed to pop up a bunch so maybe the latest version is a bit more solid for you.  Since I don't work on this full time it gets hard for me to stay on top of it as much as I would like.

Thanks for the update and feedback! Finally got around trying out the new version. Precision update accuracy is a great addition, for me a value of 3 should be good enough. However I had 2 problems at the start:
1. The location precision update does not use the value which was given on the ui, only the cleanup vertex which means that my sectors get displaced because of the original 1 decimal accuracy.
2. For some reason a vertex Y coord of -4.25001 results in -4.251 after rounding. Also, I do not know why these odd values even exist.

1) I must have missed the sector placement precision cleanup,  easy fix.    Thanks for catching that and letting me know!

2) Floating point numbers are never precise which is why I had the rounding set so high.  It seems to get more inaccurate the longer the number is after the decimal point which throws off the Boolean operations and gives errors or incorrect unions.  In the old days of Doom they used integers for pretty much everything.  If you were able to get away with using only whole numbers I believe you would see fewer if any errors...but the scale of your map would be pretty big and chunky.