Seems like the most likely cause, espeically on a site dedicated to changing the stock version. But, with many people reporting similar issues on different phones and using manufacturer ROMs it seems less likely.
Quite likely I thought, may still be an issue in tandem with the dust issue. However, I was able to confirm a fix without changing any software.
Crappy proximity sensor chip (CM3602)
I work in the semiconductor industry and know how much effort goes into qualifying devices for manufacture, whilst this isn't impossible, it seems unlikely to me.
Cases & Protective films
I thought this was probably the likely cause, so I downloaded the Android Sensors app and tried cased/naked. It makes no difference, which rules this one out.
Dust in the works
As per this thread I thought I'd give it a try. Bingo the Android Sensors app now responds to my hand moving towards/away the speaker grill. Calls now work okay and I can even use the keypad to access my voicemail.
SOLUTION - vaccum your phone. It fixes it!
Cheers to moerph and puiloong for pointing me in the right direction.
PS I'm using 10.1-20130402-EXPERIMENTAL-u8815-R3 (not that this is relevant, it was the vacuum that fixed it!).
PPS Apologies if I'm stating the obvious, but it took me a while to find this fix.