It seems that the totals don't add up in the Gene Ontology term enrichment list analysis widget.
I have 96 genes in my list created by searching for "root hair" and narrowing it to genes.
The GO widget says 23 is the "Number of Genes in this list not analysed in this widget." The flymine documentation says this number reflects genes that don't have any GO annotation.
In the GO widget, click "view" and "view results" to get a table with 2245 rows. In the DB Identifier column, click for column summary. The histogram dialog says at the top, "67 gene identifiers".
Note that 96 - 23 = 73 not 67. Six are unaccounted for. What's up?
The missing genes were masked by the p-value threshold
I found the answer to my own question. The widget is correct, it turns out.
The missing six are genes for which the GO enrichment was below the threshold for significance. The widget itself sets threshold to 0.05 by default. When I set the threshold to 1.00 and repeated the steps above, I got 73 genes in my list.