It seems that these dialects were created in the Middle Ages from a previously quite unified Basque language, and the dialects diverged from each other since then as a result of the administrative and political division that happened in the Basque Country.
In Álava, Basque had all but vanished from the Plains and the Highlands, remaining only in the stronghold of Aramaio and bordering fringes of Biscay and Gipuzkoa, while in Navarre the scholar collected the last live evidence in areas extending as far south as Tafalla.
However, cross-dialectal communication even without prior knowledge of either Standard Basque or the other dialect is normally possible to a reasonable extent, with the notable of exception of Zuberoan (also called Souletin), which is regarded as the most divergent Basque dialect.
The smaller-type instances are cases of the name being recorded for a particular area, the larger-type instances show super-regional forms common throughout the dialect area in question: Comparing the forms of the Basque verb used in the different Basque dialects also gives a good overview over some of the differences and common features.
Basque dialects all diverge from this standard inventory to a larger or lesser extent.