It's not that I don't like buttons, it is just that setting up toggle switches is simply more work than just handle a straight-forward map. But generally, a map with toggles are preferable to having multiple maps of the same location. The linking system in the atlas is primarily designed to link different locations together, and doesn't work as well when linking two different versions of the same map together, primarily because there is no sensible way to indicate a linking spot on the map itself for that purpose, so it will only be in the sidebar (or below the map in the web version viewer)

Which color are you assigning them?

Based on your description, it sounds like you may have manually changed the palette for your map, and then assigned them this color. While there is technically nothing wrong with this, the palette in CC3+ can reset to the default map palette unless it has been properly re-attached to the map using :CC2PRESETS: after any change.

The recommended way to deal with Color Key is to give the entities Color number 6 in the palette, this is one of the default colors that appear in all official palettes, and shouldn't change even if a new palette is loaded or the current one is reset.

MPEDIT doesn't show the current properties of entities. It always shows the currently active properties from the status bar, basically, it shows the settings that will be applied, not the current setting of the entities.

(And also note that MPEDIT only applies the settings when hitting OK if the checkbox for that setting its set)

A different way to check things is also just to hide the relevant sheet. Expecting everything to be on BUILDINGS?, well, then simply hide that sheet and see if anything remain (Or hide all sheets but that one, which is a nice feature int he sheets dialog I like to use)

Hiding all sheets but one is also nice when working, because that means you can do selection "by all" to grab all the relevant entities instead of trying to select the relevant ones individually

Some of your buildings are on the buildings sheet, but a lot of them are on the SYMBOLS sheet instead. Looks like all the ones not casting shadows in your image is on the SYMBOLS sheet.

The best tool to check this is always the LIST command. It reveals all the needed information.

These values and their use can be a bit hard to understand, so let me throw in some explanations and see if that clears things up. Let me know if things still doesn't seem to work as expected after taking this into account.

• Inclination is only used for roof shading, not the shadows cast from the buildings. No matter what you set for inclination, the length of the shadows will be the same, but (assuming you use a city style that supports shading - most do) you should see a bit variation in the shading of the roof. This is combined with the steepness of the roof, so the actual effect can vary, but you should see parts of the roof getting lighter/darker when changing this, but it will have no effect on the shadows cast on the ground by the building
• The blur/transparency setting are only for dungeon lighting. It is possible to use in city maps as well, but it will have no effect as long as you don't have any configured light sources in your map, and the appropriate Point Light shadow effects set up on your sheets (which are not in city maps by default). Without this setup, these settings do absolutely nothing for your map.
• Azimuth, on the other hand is directly used by the "Wall Shadow, Directional" effect, IF the effect is configured to use global sun instead of a fix angle (It usually is). Thus this setting will change the direction of the shadows cast by the buildings.