The list of countries wasn't defined by Congress beyond Iraq and Syria (presumably thanks to those being specifically called out in the name "Islamic State of Iraq and Syria"). It did include provision for the Secretaries of State and Homeland Security to designate additional countries.
My gut feeling is that the current administration didn't choose to target the same countries deliberately, but rather chose to incorporate the prior legislation by reference as a defence against legal challenges.
The EO wording is that "immigrant and nonimmigrant entry into the United States of aliens from countries referred to in section 217(a)(12) of the INA, 8 U.S.C. 1187(a)(12), would be detrimental to the interests of the United States". The referenced legislation is here: https://www.law.cornell.edu/uscode/text/8/1187#a_12 .
Have you traveled to, or been present in, Iraq, Syria, Iran, Sudan, Libya, Somalia, or Yemen on or after March 1, 2011?
https://www.cbp.gov/travel/international-visitors/visa-waive...
Please note that I really don't understand the details of the visa process in general or this program in particular, or how DHS arrived at this list of countries. I'm just submitting it as an pre-existing list of countries the DHS has expressed concern about with respect to immigration and visas. Nor do I have any reference that this list was used for the Executive Order. That said, it does seem reasonable to imagine that similar reasoning was used in choosing the countries listed in the Executive Order.