few things you can try...
1- if you have a gate valve on your skimmer put a micron bag at the end of it this will take out ALOT of the micro bubbles and your baffles should clear out the rest.
2- on either your first baffle put a few bags of carbon and the other baffels on the return pump side put some filterpads (I use fluval 404 filter pads)
3- slow down your flow I think on melevs reef he says your flow in the sump should only be 5 times your display tank size.. I like option 1 and 2 better
Probably more solutions but 2 is what I did and took out pretty much all the micro bubbles and I have some carbon in the system now as well.