Hi monochromepengu,
The rim of the condom should be as close to the base of the penis as possible; although, what you and your friend are experiencing is not unusual at all. With the measurements you gave me, it doesn't seem like there is a problem. Have you experienced the condom slipping off during sex? If so, then you might be putting on the condom inside out or it might not be the right size. Also, if your partner is uncircumcised, it's common for the condom to not go as far down to the base as it does with a circumcised penis.
Here are two resources of ours that explain proper condom use:
Condom Basics: A User's Manual and
All the Barriers! All the Time! That way you can double-check to make sure you're doing everything right! Please let me know if you have any further questions.