> Have been importing/adding the tables for the subdomains from the live site in to the local database.
This does not give me enough information. You cannot just copy a set of database tables from one WP instance and paste it into another WP stance (unless you really know what you are doing). That is why you are having problems.
Let me give you examples of how I migrate db data from production to test/dev WP instance. I do it multiple ways depending on what I need:
1) I export production database. I search and replace the prod url with the test url, prod.com -> test.com; then import it into test database. This way my test.com WP instance is exactly like my production but with a different url
2) I export production database and then import that into my test database. I modify my desktop /etc/hosts file to have all my production urls point to my test WP instance. This makes my test WP instance identical to production.
3) partial prod export. Sometimes I only export one site from prod to test/dev. It is a huge manual process that I have scripted.
FYI – this is probably more pertinent to you. There is a table ‘wp_blogs’ that stores all the sites info. You probably need to copy it over and possibly modify some values before importing to dev. I would be careful, the main domain info is in there too.