[Q] Mic not working on calls but works when on speaker. A software problem?

I am having an issue with my Nexus 5 and I can't make out what the fault is (before you shout that I am in the wrong place, please read to the end. My conclusion is not phone based. Nor is my question)
My mic does not work when I make or receive a call normally so the person I am talking to cannot hear me. If I switch to speakerphone the mic work well and I can be heard on the otherside.

I have done pretty much everything - root, unroot, flash stock, change build.prop, go from ART to Dalvik, go back to kitkat from lollipop and back again etc. etc.

I have googled extensively and it could be one of these:
1. Noise cancellation microphone
2. Earphone jack that doesn't recognise when the earphones are removed
3. A hardware malfunction.

The thing is that I have tested all of these.
1. Covering the noise cancellation mic or fiddling with the build.prop makes no difference
2. I have tried to turn off the headphones while they were in using an app from the play store. Didn't solve the problem
3. Installed a noise meter app and when I blow /tap straight on the grill were the mic is house, there is recognition. Also tested using Google voice search. Also recognised some words. Finally, if i make a call and put the phone in speaker mode the person on the other side hears me loud and clear. So not the hardware (I don't think).

I google some more and noticed that a number of phones have this issue not just the Nexus 5. For example the

** the OnePlus One (),
** the Moto G (),
** the HTC One X (),
** the LG Optimus (),
** the Xperia Z (),
** LG G2 (),
** Nexus 5 (),
** Nexus 4 (),

And probably many more...

So, could this be a broader problem with Android software itself? A universal bug? A virus? I have too many questions.

Hopefully somebody brilliant from this forum will see this and apply their genius minds. And fix what has hitherto been unfixable. Now there is a challenge - fix the unfixable.

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