It is not necessarily older versions that are more expensive. Different revisions (
http://zeldaspeedruns.com/oot/generalknowledge/version-differences for the most notable one for this) may have different features/bugs/whatever and that plays into what people want. This is also before we consider the crazy collectors that care about label quality and such like.
Equally it could also be it was priced at the time it came in and then another price was cooked up when another came in but the first was not revised "because someone will pay for it".
That said seal differences are covered
http://gaming.wikia.com/wiki/Nintendo_Seal_of_Quality
Both have USA serials and logo styles so it is likely not a different region.
It would seem then the $5 is the older of them as it uses the older logo, indeed the later one was from a several years later revision of said logo if the above link is accurate and that is the first revision of the seal text (I can't quite read it but the lengths and character shapes match what I expect).