Zone fill fails to connect to some through hole pin pads, not others

[itsko]

Seen here, GNDREF, left connectors (P3,4) are filled, right connectors (P2) are not:

All pins are correctly associated with GNDREF net.

.

Seen here, there is no other copper on another layer:

.

Placing a trace between the copper and pad and rebuilding did not resolve —
the trace merely remained.

[mf_ibfeew]

The right-side connectors contain a much tighter pitch-interval than the left-side connectors. There is not enough space for connecting the thermal spokes to pad 2+5 on the right side (without violating the drc-clearance rules).
possible solutions:

• zone parameter: clearance value smaller
• zone parameter: minimum width smaller
• zone parameter: thermal spoke width smaller
• pad parameter (for v7): doubleclick the unconnected GND-pads → get Pad properties dialog → panel "clearance overrides and settings–>set Spoke angle == 0°. This change builds horicontal spokes on the relevant pads (there seems to be enough place left+right of the connector-footprint). Be aware: if you later update the footprint from library this change will be overwritten and lost
• routing: manually route the connection to the GND-pads
• global drc-constrains: reduce copper clearance value

as a remark: Solely relying on the automatic connection of GND-pads (without knowing the advantages and risks of this behaviour) is a little bit dangerous. If you get unlucky the automatic GND-connection with a zone-fill only connects with a small piece of copper, or with a very long copper-loop.

[itsko]

I went with pad parameter:

After using [B] to update fill, everything looks great: