There can be a combination of reasons your links were not live.
1) even though the blog is auto approve, the page may not exist anymore
2) the blog owner may have changed his comment approval policy
3) Scrapebox didn't really submit the comment. I've had this happen. SB said it successfully posted the comment, but when I checked the page, it was not there. I manually put in a comment and it immediately was on the page.
Don't worry about any of these, just keep building backlinks. This is about volume, not quality.
And be sure to use the "check links" button on SB, you'll find that even fewer than you 10% are really live. I have a "verified link" success rate of about 1.5%. I have been doing comment runs on 50k URLs each time and get 1300 to 1800 verified links.