I suspect your problem is not the charge controller nor the batteries, but the way that the panels are wired to the controller itself. Check that you have the panels and the wind generator wired in parallel and not in series (effectively turning 3 x 6A panels @ 12V into 1 x 6A panel @ 36V and hence overloading the controller -- remember that solar panels are generally constant current rather than constant voltage devices). If you are wiring 3 panels and a wind generator in parallel then you will need either reverse current protection in each panel, or a set of current regulation diodes (I would plump for nice big ones in a waterproof housing with a f**k off heat sink) to prevent the wind generator pushing current backwards through the panels.
I don't have any real knowledge of that particular charge controller, I use a morningstar myself (after comparing the powertech vs morningstar vs plasmatronics options) and googling for a manual on line didn't get me anywhere but here are some other things you can try:
* Get a battery charger, around 4 amp output should be fine, and test the open circuit output of it with a multimeter (set to DC volts). This should be around 13.6 - 14.4 volts or thereabouts.
* Connect the battery charger to the input of the charge controller. This might seem odd but it at least allows you to test the output voltage of the controller. Make sure you have + wired to + and - wired to -. You should see around the same voltage output from the controller as input to it.
If you get this far then your charge controller is probably OK. You could test by wiring the charge controller to the batteries again, again making sure that you wire + to + and - to -. If you blow fuses again then you have a faulty charge controller, take it back for a replacement. If everything works then your charge controller is OK and it's time to check the panels, wind generator, and wiring.
* Connect your panels together ready to connect to the charge controller, and test the open circuit voltage of them in full daylight. This should be about 14 - 16 volts but may be as high as 20 volts (but not as high as 36 volts -- if it is then you have definitely wired your panels in series and need to fix that before you go any further).
* Test the open circuit voltage of the panels again at night, with the wind generator tied off. You should see less than 1 volt.
* Untie the wind generator and test the open circuit voltage again, on a windy night. Again you should get about 12 - 16 volts, maybe more. If you get much less than 12 you have a reverse current problem with your panels. If you get much more than 20 then you have a faulty wind generator. If you get a steady voltage around 13.6 volts then your wind generator has an internal regulator and you should either wire it directly to your batteries (and not through the charge controller) or you should disable the internal regulator before connecting it to the charge controller.
If you get this far:
* Connect everything up, on a sunny day with the wind generator tied off. Test the output voltage of the regulator. It should be a steady voltage between around 13.6 to 14.4 volts. Anything outside this range, you probably have something wired up incorrectly, check the manuals.
* Check the output voltage of the batteries. It should be around 12.2 to 13.6 volts.
* Make sure you're wiring + output of the charge controller to + output of the batteries, and - to -.
I hope that helps.