I just read the article you linked. It mentions $15,000 in equipment missing. If that is the sum of all thefts, then it is chump change and would be handled by the local PD. But perhaps the person quoted only knows of that one item and there have been repeated thefts totaling millions. Still, that hardly warrants callin in the FBI.
Maybe the article stolen is an innovative, brand new communications technology that would be of great interest to our enemies. That would justify the FBI but more likely DOE or DOD.
If paid for with Federal Grants or contracts, it becomes an FBI matter.