The sentence that shows the correct subject-verb agreement is the second one: Each cloud that produces tornadoes is different from regular clouds.
Still, while the subject-verb agreement is correct, the second part of the sentence should be the same as in the previous one "different from regular clouds" instead of cloud*.
Nevertheless, there is subject-verb agreement. Subjects and verbs must always agree in number, be it singular or plural. The basic rule is that if the subject is singular, then the must be singular; if the subject is plural, the verb must be plural.
When the words "no", "each" or "every" appear before the subject (in this case "cloud", then the verb must be singular. In the second sentence, the subject each cloud addresses every cloud singularly to check if it satisfies a condition, so the verb is singular.