If it's a umo/umo+ it most probably it's that the gears and shafts ain't perfectly aligned, then the gear 'clicks' when it fails to move, like on car gears that click. Basically the gear riders over the pulley and clicks.
http://www.thingiverse.com/thing:8781
Check that link. See the purple thingy? The gears must be on the center of the shaft. I had this problem with my iMakr assembled umo+ and figured out how to fix it by googling like mad.
Now my 3 machines don't make any weird click
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Nicolinux 288
No idea really - it is hard to pinpoint it. You could shoot a short video, upload it to Youtube and post it here.
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