Join Tables only works if there is only one field in a table set with the Checkbox option, which creates its own junction table. For example, when checking MySQL's input, if there is only one Join Table field with Checkbox set, it inserts the correct corresponding ID (starting with 1 for the first entry) into the "from" field in the automatically created junction table.
But if there are two or more fields with Join Table and Checkbox selected, then the plugin will always insert a "0" in the "from" field in its junction table, no matter which entry it is.
Is there a fix for this?