I'm confused about whether you are referencing a Gmail *account* or are using a GMail *mail program* or if you are using Apple's Mail program.
Assuming, for the moment, the latter, the first thing I'd look at is what rules you have in place. Email comes in, rules get applied, then all the email that passes the rules goes into the inbox or wherever they've been assigned to go by the rules.
So if you're seeing Mail retrieve say 10 emails but you only end up with say six emails, it's likely that you have rules set to automatically delete or move emails that meet certain conditions and it is removing them before they get to your inbox.