As José pointed out, the first sentence is wrong. It has a verb ("is") but no subject. You can change it to make "what" the subject, you can introduce a pronoun "it" to act as the subject, or you can, as in José's first example, introduce "that" as a subject. Here are some other options: "What is it that flashed on the screen?" "What flashed on the screen?" To see the difference between the sentences, remove all the clauses and strip them down to their core skeleton: SUBJECT + VERB + (OBJECT): (1) What is that? (2) What has flashed? That is a significant difference in emphasis. #1 focuses on the unknown THING: What is THAT? #2 focuses on an ACTION ("flashed") that has been done by an unknown thing.

"What is that that has flashed on the screen?" "What is that flash on the screen?" "What has flashed on the screen?".

The first sentence, at least in my opinion, emphasizes a specific fact or truth while the second implies the distinct impact of an occurence on the present status.