f.lux doesn't work anymore since Cydia Substrate 0.9.6100
Saurik updated Cydia Substrate few days ago :
0.9.6100 blocks extensions on iOS 9 that are guaranteed to crash some key processes (such as Cydia), will inject into too many processes (due to a mismatched filter), or which will lead to subtle bugs (by invalidating the codesign of the target process).
This new version also fixes some issues developers were seeing attempting to hook functions in particularly well-sandboxed processes, and adds support for the latest version of Cycript (which now runs Substrate as an injection vector).
And here is a comment about saurik on why a tweak shouldn't be working with that last update:
That probably means it wasn't working before the upgrade, but you didn't notice yet: people have been reporting tons of subtle bugs all over their operating system due to entitlements being invalidated by extensions that were compiled incorrectly (not just for iOS 9, but were never compiled correctly when they were first released, but where the effect was mitigated by a kernel patch in the older jailbreaks); I now filter those extensions and block them, putting a message into the system log explaining which of my various checks failed on the library.
Since that update, my screen is blueish again and it's awful.
When opening f.lux app, preview doesn't work anymore. So I guess that change in Cydia Substrate break something one your side.
On a side note, your beta repo doesn't seems to list your tweak anymore
We do not use substrate.