Layers, and the way they work, is a commonly misunderstood topic. This FAQ explains the subtleties of linking layers in symbols to those in designs, and covers the restrictions to colour files which may make them appear to malfunction.
Firstly, let's consider how symbols work. Whether you are looking at a pcb symbol, pcb design, or pcb technology file, when you go to [Settings], [Design Technology] and look at the 'Layers' tab, every layer should be assigned to a layer type. If any are not, as we shall see, there's a potential problem there. Each layer is also assigned to one of the sides, [Top], [Inner] or [Bottom]. Because of the need to correctly identify layers when flipping components, only one layer can be assigned to each layer type on sides [Top], and [Bottom]. This restriction does not apply to [Inner] layers because there's no need to change an inner layer when changing sides.
When you place any structure on a specific layer within a pcb symbol, it is not the layer name which the program uses. Only when the structure is on an inner layer, and more than one layer of the same type exists, is the name used as the last way to differentiate between layers, but in practice, this situation almost never arises.
So, when you place a component into a design, the layer structure of the associated symbol is compared to the layer structure of the design, and matched, not by layer name, but by layer type and side. That is why it is so vital to assign layer types to layers.
If no layer matches structures within a symbol, normally the mismatched information is ignored, but with a few early symbols, because of older data structures, confusingly they may be placed on a best fit layer.
This is where technology files become useful. In the same way as a style sheet defines defaults for a word processing document, a technology file defines defaults for a design or symbol. In the case of a design, the information is simply copied when the design vis first created, but symbols don't hold as many settings, so a technology file provides any missing information to the editor. That means that the ideal scenario is for a user to create their own custom technology files, either by modifying existing ones, saving a file as a technology file, or, if you're really keen, starting from scratch! This allows a degree of standardisation otherwise difficult to achieve. It's even possible to use [Settings], [Technology Files] to transfer relevant information into older designs where it may be missing.
Secondly, looking at colour files, you'll find that these use the simpler, and more obvious approach of simply matching layer names. At first sight, this seems a good idea, but in practice it does have limitations. The most severe of these is that layer names must match exactly when loading a colour file, or the colours are simply ignored rather than being applied to the current design (or symbol). The most obvious example would be where a source file for the colour data used a layer such as 'Top Copper', but the destination used 'Top Electrical'. Even something as trivial as an extra space is enough to cause a mismatch, meaning incorrect layer names are the usual cause of reported 'bugs' when colours fail to import as expected.
Fortunately, the same limitations don't apply to the other types of structure, as these are defined internally, but it's still possible to be caught out in other ways- such as the names used for a layer span for vias, for instance.