Low following numbers may be due to:
1) wrong FL settings.
2) FL bug - the software stops following when reaches certain amount of scraped users. For a very long time the number was ~200k. Now they say it's 500k (never test it my self).
3) Slow proxies.
4) VPS resources are to low to handle all your tasks.
We need way more info to figure out where's the problem.
In order to solve the issue number "2" you can can scrape your lists apart. Then split and import them for following. Basically, here you have two options:
A) Create new project. Use new accounts and proxies dedicated to scraping only.
B) Create new project. Use same accounts ant proxies you are using for following/unfollowing and tweeting. You can scrape at the same time when you run other tasks/projects.
Personally, I'm using option "A" because this way I can crape way faster. For scraping I run 20 accounts. 2 accounts per proxy. In 24 hours I easily scrape 600k -1M users. Then I export my lists and split them in to smaller peaces. Then I import them in to my follow/unfollow projects. Obviously, you should stop scraping with these projects. Also remember the limits mentioned above.
Settings for scraping project should be something like:
General > automation interval 90 -120 secs.
Global > scrape user
Scrape user limit: 499
