HI!
Oh, I see. You do it reverse way. Actually you are using rigctld as wsjt-x starts it anyway.
Check with console giving command :
ps ax | grep rig
while wsjt-x is running. There should be only ONE instance of rigctld running then. (one line)

Is there a special reason for doing it that way? Do you use different rig with wsjt-x than with normal qsos?

If k3 is your digital rig, and Radio 1 is some other model, I would set up Radio 2 with k3 parameters. Then change wsjt-x settings/radio to Rig: Hamlib Net rigctld and Cat control Network server localhost:4532
When first switched to Radio 2 I would then start wsjt-x without any parameters (or you can keep -r k3 if you made radio settings change with that setup)

If you have same k3 for wsjt-x and other qsos then just forget Radio 2 completely. Do changes above to wsjt-x/radio settings and just simply start wsjt-x always after cqrlog is first running. After doing wsjt-x qsos just stop it and do other qsos and start again when you want to keep wsjt-x qsos again.
No need to switch radios in cqrlog TRXControl as long as it is running first. If you close cqrlog, but keep wsjt-x running you will see that it starts to complain about rig. That reminds you to keep cqrlog running while working with wsjt-x

3rd way, if you like to work with wsjt-x alone without cqrlog is to keep your -r k3 config for that but make another wsjt-x startup icon that starts it without parameters. In that wsjt-x settings/radio you can then use those values above and so this wsjt-x needs always cqrlog running first on background. In this case it is also possible to start wsjt-x from cqrlog remote.

Se also this: http://www.saunalahti.fi/~sakny/bin/cqrlog2/setting_rigctld_for_all_prog...

How ever if you like keep everything as it is now try to set preferences/TRXContorl/Radio2:
localhost, port 4532 (these are default)
Rig: #2 Net rigctl
UNcheck "Run rigctld at program start"
Other settings as default, serial port can be empty.

and look if that makes any improvement for logging.