Verbs only ever agree with subjects. Работы isn't plural-nominative(By modern standards: ) its singular-genitive. In the past (Old Church Slavonic times), работы would be in the 'dual' number, and the verb would agree with it in the dual. They had singular, dual, and plural, with verb forms that agreed to all of it, as well as all the cases for all nouns' endings. But when the dual-number's endings died, it was approximated into genitive(because after a while it started to look the same in most cases) . I'm not sure if russians still consider nouns after "two" to be in a remnant-dual-number, or if they're just inconspicuously considered in the genitive. I would think that the modernday subject would be... два? были makes sense if you think about it, but it doesn't really match up with the strict matching system of the cases. Sure, there are two things, but neither are a subject of the word быть.