Compound paths lose colour

A strange thing happened just now that I don’t recall having seen before.
I have a number of simple objects, all the same fill colour, no stroke and none of them overlapping.
When I make them into a compound path they sometimes lose all their colour.
I have checked winding order, even/odd fill and that sort of thing but since none of the objects overlap, that shouldn’t make any difference anyway.
This doesn’t happen every time, so does anyone know what could be causing it?

I got before and resolved by cleaning up the original selection. Cleared stray points and duplicate overlapping objects.
In screenshot below I duplicated the cyan square and filled with none, did a compound path of 4 objects and lost the fill of cyan.
Also if you ever open a file and get a missing plugin that could happen.

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    I just want all inner shape and overlapping shape areas to be considered the composite fill of the compound shape - so in my example above, the three red rectangles lacking a centerpoint I want to contribute to compound path's composite fill, instead of knocking it out.
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