Welcome Snelly 50! I'm thinking you may be Snelly 40's dad? Pardon me if I'm wrong on that. You're right on with the assumptions that the bubbles may be caused by not enough flow through the back. If shutting off one of the 2 pumps gets rid of them that's another good indicator that the bubbles are NOT originating from the skimmer, or they'd still be getting pumped into the tank.
I've done the tubing mod mentioned by Brent - it involves adding a 3-4 inch piece of plastic flexible tubing (got mine at Lowes) over the inlet of both pumps, and then needing a 12" plastic cable tie around each pump to keep the extra weight of the tubing from pulling that bottom piece off of the pumps. I can't remember what diameter tubing is needed. Kent (SWFish has joined Reef Sanctuary, but hasn't had a chance yet to get in and introduce himself. He's the expert on this mod. I've had some success with it but would still get the microbubbles if the level dropped too low in that pump chamber.
Too much media and/or too fine of a media can also cut the flow. Here's a list of possible microbubble causes that I once put together for someone:
Possible microbubble causes:
1) Plugged up filter pad/sponge. You may have too thick a black sponge. It's often helped to cut that black sponge thickness to 1-2 inches thick, instead of the original thickness supplied with the tank. You just about have to rinse or replace the (original white) filter pad every 2-3 days to keep the flow high through the back. These fine filter pads can clog up pretty quickly (plus generate nitrates) if not cleaned/replaced frequently. You can get similar bonded filter pad material at most LFS in a large sheet form and cut replacements from that. The stuff I use is blue on one side, white on the other.
2) If you've got media under the pumps - the media or the bags that it's in may be getting plugged up with detritus, cutting flow. Remove, rinse in SW or replace. At times the drawstring on bags, or the bags themselves, block one of the pump inlets. Likewise too much media under the pumps can cut the flow too much.
3) If you have placed media above the skimmer pump, or even on the left side of the skimmer, especially a fine grained media like Chemi-Pure, these types of media can compact after a while and cut flow. Or, the bags get plugged up with detritus. It would be great to be able to keep media in these spots, rather than in the hard to access location under the pumps, but unless it's a large grained media like carbon it usually cuts flow too much.
4) Also - see if you can get a finger under the pumps to be sure that plate on the bottom hasn't come loose. Some owners have tied 12 inch cable ties around each of the pumps to ensure that fitting can't become dislodged or fall off.
5) If running a cannister filter, shake it back & forth several times to release entrapped air at the top. If the cannister has entrapped air you'll often see periodic bursts of microbubbles as this entrapped air is released periodically, and is chewed up by the pump impellers into microbubbles.
6) Is anything blocking the overflow gate? Something like a starfish or anemone can crawl over the gate, cutting flow, starving the pumps, and creating a whiteout of bubbles in the tank. If the gate is covered with a thick algae growth the same blockage could occur.
7) Is the gate pushed down all the way? If the gate is raised up too much it won't let enough water through to the back.
8) Skimmer problem - totally different issues. If the microbubbles are an "all of a sudden" occurrence, after not having many for a while, it's probably one of the above causes. In newly set up tanks, microbubbles from the skimmer should be expected for a while, till the skimmer breaks in, and bio-load is built up in the tank.
Some owners have removed all of the filtration pads & media from the back and just rely on the rock to take care of all filtration. I haven't done that as I like to use some chemical media, and I like to have the pad to catch any food and sediment that goes through the gate. Others have pulled everything but the skimmer out of the back, and hooked up a fairly large cannister filter in the cabinet, with the inlet and outlet pipes in back, and when doing a weekly cannister cleaning they fill it with fresh SW and consider the couple of gallons of water their weekly water change. This is a cool idea, but you have to keep up with cleaning that cannister or it could become a nitrate generator. I tried the cannister approach and loved it, but saw my nitrates rise too much. Others haven't had this happen though.
So there's my current summary of microbubble causes & cures. There may be some I've missed, and some that some others can add, but it should give you a start on things to check on and consider.
I hope it helps!
Terry
PS -edited several times - I'm a gud speler but a terible tipist! I only ever see my mistakes
after I send a reply