Very simple: Z100 (and any other large market CHR) of any time period (decades ago and today)
used and uses *local* research to determine what they should air and only use national charts for general guidance.
In fact, it is the results of what those CHRs play that make up the national charts, not the other way around.
There are such things as "regional hits" that perform better on certain stations in certain regions.
That would explain why some songs would chart higher (or lower) on Z100 (and other CHRs) as compared to national charts.
There are certain genres of music that may perform better in certain regions more than others.
For example: late 1980s freestyle dance music performed better in places like NYC and Miami than in other regions.
"Running Up That Hill" is an odd duck as a "bringback", such is the influence from soundtracks to today's "new media".
It was not much of a CHR hit the first time around (did not chart on Z100) and really only got any type of
semi-regular airplay on modern rock stations (such as WLIR Garden City and KROQ L.A.) and more adventurous
album-rock stations. (KROQ Top 106.7 of 1985: placed at #37. Was a WLIR "Screamer of the Week" in August 1985.)
I could be wrong, but I think the song placed at #102.7 on album-rocker WNEW-FM's year end list for 1985.
(In other words, the last position as the station's frequency was -and still is- 102.7.)
PS check this link for Z100 weekly surveys from 1983-1992 and year-end lists from 1983-2013
where there are many examples of titles which charted much differently locally than nationally: