Oh, so I should have posted in this in this thread? OK then, my bad.
Anyway, it's not the logic analyzer window that is the problem, I am very familiar with that, I use it all the time.
It that there is another window
inside the logic analyzer, an "advanced menu". And there is apparently NO information on it that I have seen. Search the user guide, you will find that in all 58 instances of the words "Logic Analyzer" not a single one even mentions this window or how to get there. Heck, search all the guides, and the internet. I'm using MPLAB 8.84, which as I check is an update behind. It may have been removed in 8.89, I haven't looked.
Anyway, here is an example of one of the options it has...
And here is the result...
And if you play with it, you will find that it is very buggy, here is an example of what happens when you try and move the fill reference level of the above options to try and make it so the fill is level with logic low.
You can see that the left corner of the fill gets moved down as it should, but the right corner stays in place and mucks everything up. This reeks of a simple bug where the dev simply missed doing the calculation for the other point. Half the other features are just as buggy also. Pretty interesting. The whole menu resets after you rebuild too, which is just as odd.
In any case, there appears to be absolutely no documentation, try finding something about it on the internet or in the guides. Like I said, nothing but crickets (silence). I also have found no other way to get the waveforms filled in like the above other than with this menu. I strongly suspect it is a remnant of a possible "MPLAB 9" and it's features, that was abandon during the move to MPLAB X. If so, it may be that there needed to be a 2011-2012-2013 MPLAB 8 user guide for it to show up in any documentation.
Thinking about pestering Microchip about this, maybe get the bugs fixed or something if they would. I don't dislike the feature. It would actually be wonderful if it all worked well.