I am not able to see the private GitHub repos that I have access to. Our team is NOT an organization in GitHub. I found a workaround for Mac, but they still are not showing up in Sourcetree for Windows... I am using version 3.2.0-beta-3444.
Hello Trevor and welcome to the Community.
We can confirm that your issue has been recorded as a bug within Sourcetree. You may find further information about this bug at SRCTREE-6653. We would ask you if this matches your issue to please vote and watch that bug.
Additionally, I found there is another Community post which discusses the same issue and has a user reporting it to resolve the problem. You may find this post at Sourcetree doesn't list GitHub private repos by default.
Let us know if the linked post was helpful and if the bug request does match your issue as well.