If I recall correctly, WMA is stored inside an ASF container. I would guess that it is the container which provides extra functionality such as index marks. If this ASF index function is standard then maybe there's a way to view or edit those index marks.
The ASF Specification contains an incredible amount of Objects, among them are several "Index Objects". Could you upload a sample file containing index marks? Then I could look into the file and maybe I can tell you then, if and which index objects are used. If you want to do it by yourself, you need to load a sample file into a HexEditor and search for the GUIDs of the index objects (these can be found in the ASF specification). But I don't know about a program that is capable of handling those index objects
Liandril, I followed your interesting link to the Microsoft info on ASF and installed their ASF Viewer ("Windows Media ASF View 9 Series").
The viewer very neatly shows a view of fascinating information about an ASF or WMA file. I couldn't find anything which related to index marks but there is some much info that I haven't checked it all out. It seems that the entry for "flags" (in File Properties Object) is for something else. ...I also looked at the Microsoft ASF specifications document which I found using your link. It seems there is something called a Seekable Flag which is used to indicate that a file contains Index Objects.
I will upload a sample audio file for you to look at. Can I upload it to this forum or do I have to upload it to the Uploads Forum?