Sorry. I've been working on some video tutorials in my shop and have been very focused on that.
The way that the software understands painted segments is that a file with an entry for every segment that is painted. This becomes difficult because when you paint a bunch of segments using repeats of more than one and perhaps a diamond pattern, the software first has to determine if that segment has been painted before and if so, it needs to change that entry. If it hasn't been painted before, it needs to add that entry and if it is being painted with the default species, it has to remove that entry altogether. This works quite well, but there are so many things that can go wrong, especially if you do a lot of Undos where everything has to work in reverse. One thing is guaranteed to confuse it. All bets are off if the number of segments per row changes. It is OK if you reduce the number of segments but if you increase it, it is likely to become confused.
There is one more thing that I suspect is the issue which has to do with the default species. If at some point you changed the default species but had already painted segments with that species, there are entries in the file that no longer should be there because those segments are now painted instead of default species. About the only thing I can do about this is give a warning that if you change the default species, it will be necessary to reset all of the painting that has been done.
I opened your plan and reset the segments and then painted two Maple segments on each with 9 repeats per row and the Summary is now correct.
Unfortunately, for me to see where the error occurred, I would have had to be watching to see what steps were taken during the original painting so I wouldn't have a clue as where to start with troubleshooting it.
The process I came up with to handle the painting of such large number of segments has to be more complicated than I would like it to be. Fortunately, I know the things that can break it and I may have to simply warn you that doing one of those things requires the segments to be reset. Fortunately, most designs can be recreated very quickly.
I created a new export file and added 'repainted' to the description so it should not overwrite your existing plan.