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If you only have this microphone problem when using this particular application I would advise contacting the application developers directly.
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In your case as it is a problem across the board, I would advise reloading the firmware as it looks like something went wrong during the update you ran:
1. Download the PC Companion software from http://www.sonymobile.com/gb/tools/pc-companion/
and install it on your PC.
2. Install and open PC Companion then select Support Zone.
3. Phone Software Update.
4. Start.
5. Repair Phone
6. Continue
7. Accept data removal
8. Next
9. Wait for prepare
10. Select Phone
11. Follow the connection steps
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I'm having problems with my microphon too, in calls a little, using speakerphone i'm having a lot of problems in a call, in a whatsapp, in voice recorder... The sound is not clean and is too low. I already tested another 2 Xperia Z1 in Stores and sight all comes with that problem... Its possible to fix it? i already actualizated to 4.3.
My problem with the Mic is when I try to use apps like SoundHound o TrackID the message application is "We can't find a Mic available, maybe another application is using it."
Hi Guys
>try using different earphones first ,check whether it works or not then you can come to conclusion is it problem with the phone or earphones
>last you can do is Restoring the phone (losing all data, make sure you take backup)
Manjuboyz 
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