I am running BOINC on a server of mine, and I set the CPU limit to 55% from the option inside computing preferences which says stop boinc when cpu usage goes beyond x% or something similar, and I also changed my computing preferences from the setiathome website to that same amount.
Sadly, boinc is being a bad guy here, and creating annoyances.
Even after setting the limits, restarting the server multiple times, and syncing it with seti@home, it still wants to keep using 100% of the CPU.
What to do now? My provider is going to kick me if this continues for some more time.

Well, don't run BOINC on the server then, or do not use that option to pause the CPU. There are plenty of other options to do so.

This option will only suspend BOINC when other, non-BOINC processes, use that much amount of CPU cycles. Project science applications are not non-BOINC processes, so they'll continue to use the CPU cycles. Only other processes, such as a text editor, are measured.

The option will only work when you actually run BOINC based on preferences (Activity menu). If it's set to Run Always, well...
When you simply want to throttle the CPU usage, use the Use at most X% of CPU time option for that. Or set up the amount of cores BOINC may use to anything less than all, if it's a multiprocessor setup.

But as you say, the server isn't yours. May I remind you of the Usage rules? Run BOINC only on computers that you own, or for which you have obtained the owner's permission.

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I found my way around it. Anyways, I rent a server, and I know thousands of other people run BOINC on their servers. Its like saying because you rented an apartment, you can't run a fan inside it.
The server belongs to me for a set period of time that I can extend upon my will, and I have resources that I have rights over, which I can use for doing whatever I like.