My fan theory is that Prof. Utonium found a source on Monster Isle which he secretly goes to to replenish his stock.
While Monster Isle is the home of kaiju-tier monsters, I imagine the island was formed over the corpse of a prehistoric Eldritch monster.
On an expedition to Monster Isle, the professor explored the underground caves and found what looked like a lake of crude oil, only to realize it was no composition he ever seen. He took samples of it home, labeling it as Chemical X.
Chemical X is actually the decayed/fossilized matter of the ancient monster. In H.P. Lovecraft fashion whenever this long dead monster can be "awaken" or resurrected would make an interesting story, especially when the PowerPuff Girls find out where Chemical X comes from.
