Tim,
You do not say how long these filters have been in service. Even assuming they are Wynn filters there is some limit on how many times they can be cleaned before needing replacement due to plugging. This limit occurs when the time between cleanings reaches a level unacceptable for you or air flow after cleaning is still unacceptable.
Peter's idea to get a Magnehelic or other meter to measure the pressure drop across the filters is a very good one. This number goes up as the filters clog. While the precise number will be debated, when it gets up to (perhaps) 4" of water column [about 0.15 psi] across the filters your air flow will start to drop off pretty quickly.
Others here have mentioned leaks which are certainly a preformance problem however they typically result in increased dust to the filters causing the filter pressure drop to rise too quickly rather than a drop in air flow unless the leak is large.
If your system passes the incense smoke test yet still will not flow air like it used even after cleaning to I would remove the filters to see if they may be *totally* pluggs with chips (it can happen if you overflow the bottom basin). If they appear clean I'd replace my filters, installing a low-pressure differential pressure meter and logging a baseline (clean) pressure drop for future reference.
In writing this, I'd probably re-install the old filters with the gauge installed to see how much pressure drop is causing me to get the substandard performance I'm now getting. This could be used to decide what pressure to use for cleaning in the future.
Just my thoughts.. my $0.02.. YMMV.
Jim in Alaska