Why are there two version of the flag of El Salvador?

No they aren't. There is only one flag. The official one is the coat of arms. The flag with the phrase “Dios Union Libertad” is the civil flag used by some state organizations. read more

There are two versions of the flag, one containing the national coat of arms with the words "REPUBLICA DE EL SALVADOR EN LA AMERICA CENTRAL" (English: Republic of El Salvador in Central America), and the other with the words "DIOS UNION LIBERTAD" (English: God, Union, Liberty); both have the words in amber. read more

Below, there is a scroll which states the national motto of El Salvador: Dios, Unión, Libertad which means "God, Union, Liberty". All of this is surrounded by a laurel garland, which is tied together under the national flag. read more