George,
As others have stated above, you must be certain there are no leaks in the dust collection bin first. But sadly, I think the main issue here is the short cone design of the Laguna cyclone. It simply is not a very efficient unit to separate the incoming air/dust/chips mixture before the air enters the blower intake and deposits a substantial percentage of the particulates into the filters and collection below it. By contrast, the ClearVue CV1800 cyclone removes upward of 99.9% of the incoming dust before air is pulled into the blower. It has a long cone and the intake chute is angled down toward the cone and has a helical ramp for the air to move smoothly, increasing the separation efficiency. Typically, one would removed a cup of fine dust from below the filters for every 5-6 barrels of chips and dust in the main bin.
But your first step is to check for leaks (every connection on the cyclone or bin that is on the suction side). I have used an incense stick (or cigarette) to generate a smoke stream that will quickly react to any leaks into the cyclone. Even ClearVue's won't operate efficiently if there are bin leaks.
Hope this helps.
FWIW, I really do not think the short stature explains anything. My 2HP JDS cyclone is very similar in design and uses a very similar, if not identical, funnel section for the cyclone and captures better than 99.99% of waste in the main waste bin. I have filled my 35 gallon barrel a good many times over the years but I have
never emptied the fines bag, which contains just a few ounces of extremely fine and powdery dust (almost as fine as talcum powder). Essentially nothing from jointers, planers, tablesaws, routers, or bandsaws will make it to the fines bag as the particle size is simply too large to get carried past the impeller. It is true that a short cyclone is not quite as efficient when it comes to separating very fine particles, but for typical woodworking it is a very small performance penalty practically speaking, especially if one primarily uses a shop vac to collect their routine sanding fines (where the performance difference is actually at its greatest).
I would also be very surprised if the use of 6" pipe is the cause of issues if the run is, as stated, a 6" run all the way too the jointer and the jointer opening is, or was enlarged, to 6" (as I believe has been implied), thus no undue restrictions to airflow, and/or an auxiliary gate was also opened to allow even more makeup air in and made no observable difference. My 2HP cyclone was designed to accommodate up to an 8" intake (though such would require a great deal of air to maintain velocity over the run length, especially if choking down to 4-6" equipment ports, but I would be very comfortable with 6" duct on a decent 2HP cyclone). That said a very simple experiment if all possible sources of leaks have been thoroughly eliminated as a possibility is to install a short length (a couple feet long to establish laminar flow) of 4" pipe just before the DC intake port which will serve to momentarily greatly increase airstream speed just ahead of the cyclone. As such, I would be very surprised if this DC could not handle a 6" line as Laguna is a very reputable brand -- but if all other efforts fail it is well worth giving Laguna a call to seek their advice and assist in the troubleshooting as this is not normal behavior for a cyclone.
But at this point everything really points to an air leak within the cyclone or waste barrel which can greatly disrupt the formation of a high velocity cyclone around the perimeter of the funnel and a much slower low pressure airstream in the center of the cyclone since the newly introduced air will disrupt the physics by adding in an uncontrolled airstream disrupting the normally laminar airflow and the proper formation of a controlled low pressure zone in the interior are critical to proper formation of the cyclone and particle separation.
Again, I wish the OP the very best of luck in resolving this issue as I know such issues can be frustrating when all you really want to do is make use of your new setup and get started on a new project!