Do you download your gmail to an email client, like Thunderbird? Or actually log into gmail through your browser?
I had problems with missing emails like you're experiencing and it turns out that Gmail has a very aggressive spam filter. It will stop it from being downloaded to your own client, not sure what it did with those emails through the browser, don't remember if I found them or not. The one email where it was an issue I finally made an extra gmail filter that stopped it from holding back any emails at all.
