You're right actually, CTF is having ranking issues. I got this in a server log:
[176311.15] Log: CustomGameTypes.u Failed - Removing Ranked Status
I'll contact TWI, either they black-listed CTF (why???), or they don't have the latest version of it (probably). Or it could just be a bug... Stay tuned.
In the mean-time, restarting your server should temporarily fixed the issue, until the crawler (i suppose there is a kinda bots verifying the server files since it happens randomly) verifies your server again.
IMPORTANT NOTICE TO SERVER ADMINS REGARDING RANKING:
If you have a ranking issue with CTF on your server, make sure you don't enable the mutator CGTMutatorWorkshopCTF. This mutator is NOT for use on servers, it is only a trick i used to allow Workshop users to change the CTF parameters from the Workshop interface. Using the mutator on your server is likely to unrank it.
If by mistake, you enable the mutator, a map change is not enough, you will have to restart the server. In that case, you might be interested to read this.
Best regards and "thank you" from about 20 players of the free weekend.
They're playing the game the first time and only capture the flag, I told them a bit about the mod and the guys who made it and they were really thankful for your work.
A few of them bought the game just for the capture the flag mod.(well...for 1$, why not )