iOS 10: Storage Almost Full Warning (But I have free space)

I am running iOS 10.2.1 on an iPhone 5S, with a doubleH3lix jailbreak. The phone was receiving the "Storage Almost Full" warning before I jailbroke it. I reset the phone to factory settings (got the error after installing one app), jailbroke it, and ran two different cleaning apps, one of which is iCleaner.

I am guessing that whatever cache iCleaner is looking at is the same one causing the warning. But, as you can see, I still have 9GB of free space on this device.

Is there a way to clear this cache and correct the free space showing in iCleaner and stop the warning from being triggered?

Solution 1:

I have reset the iPhone from the iPhone's setting (because I did not want to update the phone), but in order to truly clear the caches and space, I had to reset (and update) using iTunes.