The checker map, like any other map on Project-GC, shows a cache on the coordinates you have for it, i.e. the posted coordinates or the corrected coordinates if you have such.
Coordinates can be corrected in two ways: by clicking the coordinates on the cache page and entering new coordinates there (which is equivalent to changing the coordinates using an app) or by putting coordinates in the personal cache notes field. I *think* the first has priority if you have both. The "final coordinates" waypoint is not used by Project-GC since we can't see it if it's hidden.
It could be that your corrected coordinate change has not been detected by Project-GC, for some reason. You can request a refresh of your corrected coordinates via Support -> Self-support. Note that there are two different buttons to click for the two different types of corrected coordinates.