Trouble with SARS_CoV_2

I am slightly confused. Are you using PANGO Lineage or Nextstrain Clade? 23I is a Nextstrain Clade. In either case, non-grey colors are assigned to values defined in the file defaults/color_ordering.tsv. It is a large file, but some of the relevant lines are:

…
clade_membership	23I (BA.2.86)
clade_membership	24A (JN.1)
clade_membership	24B (JN.1.11.1)
…
pango_lineage	JN.1.4
pango_lineage	JN.1.4.1
pango_lineage	JN.1.4.4
…

Note that the metadata values must match exactly for a color to be applied. For example, a pango_lineage value of JN.1.4 (consensus call) will not match JN.1.4.