I use Ola Hallengren's scripts, never had a problem with them. https://ola.hallengren.com/

If your diff backups are taking longer, can you schedule them to run more than twice a week? They would then have to backup less changes and have a shorter run time. But I would have thought that you should be able to take log backups when a diff is running, or is that a "feature" of the third party app?