Hi Frank - the Stew-Mac water based filler which is probably much like the LMI filler gave me fits and I was never able to get good results with it. This included a guitar with an Aussie Blackwood back and sides......
What worked for me was switching to epoxy finishing resin for pore filling. System III was the first product that I tried and it worked great. It is unforgiving in the mix ratio and requires a gram scale to ensure an accurate mix. Next I tried Z-Poxy and liked that even better - Z-Poxy is more forgiving in the mix ratio. Both products gave perfect fills with two applications and any sand through was easily fixed by wiping on a 50/50 thin coat of the epoxy and denatured alcohol to even out the color. Use a lint free cloth to wipe the mixture on. Both of these products are "finishing resins" and not designed to be epoxy glues because of the thin viscosity. Be sure to get the finishing resins because both Z-poxy and SIII also make epoxy glue in other flavors.
West Systems epoxy, not a finishing resin, also works fantastic.
I guess the main point of my post here is that I never had any luck with the water based fillers but when I went the epoxy route the problems were solved immediately and pore filling was now something that let me keep some of my hair.....
Application technique is also a possible problem area until you get your technique down. I use a credit-type card (preferably without a high balance....

) and instead of using it to squeegee on the epoxy I use it to "mash" the epoxy into the pores moving in all directions but especially at 45 degrees to the grain. Once a small area is done I then use the card at 45 degrees to the grain to squeegee off the excess. Wait a day and sand it back, it sands easily and you can sand back to bare wood or leave a thin coat of epoxy over the wood. Nothing pops the figure of the wood like epoxy.
Good luck.