The smaller the nozzle, the higher the pressure in the melt chamber and the harder the extruder has to work. That means at least a couple of things need to be just right: the tension on the extruder idler and the reference voltage of the extruder stepper driver. If the first isn't high enough (the idler isn't screwed down enough), the filament won't be gripped strongly enough to pull through (although too tight and you run into other problems). If the stepper motor isn't receiving enough current it won't have enough power to push filament through.
I believe the makerfarm prusa instructions has a section on adjusting the stepper drivers.
It's also vitally important you don't get any dust working its way down to the nozzle. Clean your nozzle and install a dust trap on the filament. You can clean your nozzle by setting the temp to about 230c, letting it settle, then setting it to the glass transition temperature of your filament or just above (I think about 70c for PLA, but a quick google will get the correct numbers). Let it settle there and then pull the filament out. If you see a straw at the end of the filament you pulled out, the cleaning is working. Repeat a couple of times for a thorough cleaning. Thingiverse has a bunch of filament dust cleaners.
[
3DKarma.com] - suppliers of quality, affordable 3D printer kits and filament for the UK market.