Hi Emma,
Bringing this topic back from the dead. We recently came across this issue after upgrading to 3.3. We use only the "Course Upload" using a .csv to bulk upload our courses. We do not create a new course prior to using the .csv. During the .csv upload we enter the templatecourse parameter to point to a course to grab the content from. Prior to the upgrade, this would carry over our access restrictions at the topic level. Now the sections come in, and all other non-topic based restrictions carry over, but the topics access restrictions remain blank. Topic custom titles carry over fine.
We spoke with our Moodle host, and they did some testing in their old versions of Moodle claiming that it never functioned like that. They found that when using the backup/restore process to a new classroom that the restrictions will carry over. However, we've always used the bulk .csv course upload process prior to this 3.3 upgrade, and we've never had an issue with these restrictions before.
I did find an old reported bug on the tracker that may be related: MDL-52890. Sam's comment makes me wonder if the upgrade changes based around numsection could be related to the issues are facing.
While our University didn't have any consistency issues prior to the upgrade, it makes me curious if there is some deeper cause or lack of understanding on our end. The real question is why would this work with a backup/restore, but not with the course upload via .csv? Is there any solution? Are there any users out there that are able to successfully use the "Course Upload" by .csv and have their topic restrictions carry over?