Mark- the prox switches "should" get about 0.002" worst case repeatability if they are set up correctly. Typically they get 0.001" on various shopbots I have checked for both X and Y.
Prox switches are very immune to dirt, so that is not the factor. Check the gap. Also read Brady Watsons recent post (just a couple days ago) on getting maximum performance from the prox switches, excellent advice there.
Start there, if you are not getting results that good, the gap between the prox switches and the bolt heads is the most likely culprit.
D
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