I think you have several issues involved here
1) when things are running ok - weewx has a PID of 343
2) there is no explanation of why a new version of weewx with PID of 326 is started - but the clock is wrong - so from this point onwards you will have very mixed results!! With an RPi you should install a real time clock for consistency as time is vital to correct running of weewx.
3) now you start with PID of 326 and 331 and finally the clock updates
The error will relate to records already in the database with the same time as the new record - and the cause will liely be connected to wrong clock times somewhere along the line
In all it looks more like an RPi problem - possibly power supply related or possibly indicating an impending failure of the SD card