Despite setting player colours in SCMDraft, they are showing up as default colours (P1 red, P2 blue, P3 teal, etc.). It always happens this way, it is not random like it would be if 'Randomise Start Location' was ticked. Any reason this would be happening?

Are you saving the map as a .SCX? .SCM does not support color changes.

Are you opening the the map in an editor that does not support player colors afterwards? (ex. a staredit.exe based editor)

No and no. SCX, used StarEdit to import wavs but the colours were manually reset afterwards.

Making a second copy of the map resolved the issue.

I've noticed sometimes I will have to make changes to forces / player settings twice and re-save before SCMDraft will actually keep the changes. Just a little annoying thing that happens sometimes.

I made extensive attempts to do just that and it didn't result in any change. It was probably due to opening it in Staredit once but I didn't get that error with another map. There could be a filesize limitation that causes issues with editors though, it is over 300 megabytes.