Why is it so popular to say that it was a box when it was actually a jar?
Essentially, the same reason why any other misconception is popular - it rarely gets corrected enough, and the consequences of the misconception are minuscule.
First, it originated as a mistranslation by Erasmus, on account of whom others, especially poets and painters, represented the jar as a box. Once something gets into the popular imagination, it's difficult to leave. Just look at the featherless, fatless dinosaurs in Jurassic World.
Apart from the visual aspect, "Pandora's box" has now become a saying, and saying's are notoriously difficult to change, even when wrong.
Also, though, the type of jar mentioned, a pithos, is meant for storage, and is often plugged up with cork and wax. However, the action of snapping the lid quickly doesn't exist for a pithos, so when recalling the memory of the story, the vivid actions tend to override the more inconsequential details, leaving the incorrect details in the retelling. From there, it's a simple snowball effect.
The Adages of Erasmus, ed. by William W. Barker, Toronto: p. xxxix
Also, Wikipedia has a few paintings, showing it's early popularity. Interestingly, I remember Tomb Raider: Cradle of Life also had Pandora's box (as a wooden jewelry box) in the movie, once again demonstrating the visual aspects.
C.M. Weiner has provided an admirable answer.
The difference in volume between a pithos and a pyxis may also reflect an ideological difference.
Notorious for their misogyny, archaic Greeks viewed women as much more pernicious than Renaissance humanists did. As a pyxis is less than capacious (of evil), so too is womankind according to this Christian intellectual.