All four of these had military bases. In the case of Monterey (Fort Ord) and Merced (Castle AFB) the military bases were BRAC'ed a decade ago.
California had a literacy test. At the time the test for Section 5 coverage was made, the California Supreme Court had enjoined use of the literacy test since it was in English only, and California repealed the law soon after.
Because most of the soldiers were young and temporarily resident they did not vote in those counties, if at all, nor bother with the goofy procedure of faxing to the Census Bureau proof that they had voted elsewhere. The four counties failed the participation test (based on turnout vs. CVAP). This didn't happen in San Diego and Orange County, since while the military bases are quite large, they are not as relatively large to the overall population.
Merced County may have missed meeting the threshold because the census bureau overestimated the CVAP (by assuming that all migration was by citizens).
Twenty years later, Monterey County was considering deliberately including Fort Ord and Soledad Prison in a Salinas Valley commissioners district, because the soldiers still did not vote and those in the prison could not vote, but they would pump up the total population and also make the minority population share higher.
Now Section 5 is used as a cudgel to derail other elections, including the 2005 special statewide election, and the special election to replace Abel Maldonado - in that case there was a deliberate attempt to deny the Central Coast senate representation during passage of the budget. So much for voting rights.
Section 5 is based on:
(1) Presumption of guilt - covered States and entities must prove their innocence;
(2) Corruption of blood - covered States and entities are designated based on elections nearly 50 years ago (while in hellholes like Hawaii, Washington, and Minnesota relative voter participation by minorities is much worse than for Anglos)
(3) Infringement of State sovereignty.