I have this same problem.
I have reset and re installed the rom via pc companion and same problem.
Basically the phone will not charge via the magnetic connector at all.
if you switch off the phone it will not stay off, it keeps turning its self back on again and boot looping: displaying the sony logo, then off, then sony logo again.
If you hold the power button down for 20 seconds whilst on a Sony logo, the phone boots to the experia logo and boots normally.
Problem is the phone will NOT switch off and half the time it wont come back on. Its basically a lottery on whether the phone will come back at all.