If I go in the progress page and check the total number of items studied since I use skritter, I get:
567 Words
1049 Characters
1009 Tones
The total numbers of items should be (567 * 2) + 1049 + 1009 = 3192, since the words count both for C and T.
If I go in the viewer and I keep clicking on "Next 20" until I reach the last page, I have a total of 2508 items.

It is possible that some item have been lost? Some days ago I started practicing a chinesepod list, the word 问题 was added as a new word, but I was quite sure I had already studied that word.

P.S. In the viewer, If I click very fast on "Next 20", I get a wrong total number of items at the end of the viewer, like 3858. I had to click and wait until the page was completed loaded, to reach the end of the viewer with the correct total number of items.

Sorry, I've found that in my viewer there is the word 没问题, so I'm not so sure that I had already studied 问题, maybe I had just studied 没问题!

Pulling up the data raw I get (today, so somewhat updated):

HISTORIES:
char_rune 1064
char_tone 1025
word_rune 585
word_tone 574
total: 3248

And if I actually go through and count the number of items you have:

ITEMS:
rune, both: 623
rune, none: 471
rune, simp: 480
rune, trad: 1
tone, both: 637
tone, none: 482
tone, simp: 493
tone, trad: 1
total: 3188

And of those, 7 have not been studied, so they never had any effect on your progress history, or they haven't yet.

Note that items and histories are subdivided a bit differently. But it looks like your missing numbers are several hundred items that don't come up on their own, mostly individual characters. Items with styles 'simp' or 'trad' only get studied when their respective style is being studied, 'both' items are always studied, and 'none' are ignored/deleted. And if an item doesn't show up for study on its own, it doesn't show up in your viewer or queue browser, either. But items with style 'none' can still show up if they are part of a word that you add and are studied as part of that word.

So in practice the system goes like this. You add a word composed of several characters. The items for the individual characters get added as well, but with a style of 'none', so that they don't show up on their own, but their progress is still kept. Now when you study that word, the data for the individual character gets updated, and as you learn it as part of other words the progress reflects that. But the character never shows up on its own, so it's not considered part of your schedule unless you go and add it in particular.

The end result of this is I believe your progress is counting only about 2% higher than reality. This may be errors that accumulate over time or were the result of a temporary bug. Since there are actually almost 1000 ignored items, you should have only gotten about 2200 on the viewer, so I'm guessing that is from the same bug you got when you clicked next quickly.

Does that all make sense? The progress counts learning that's secondary to what you have scheduled for study, but the viewer only shows what you are studying primarily. That's the gist of it.

Thanks for the explication, Scott.