I found the problem!
Since the 'text_list' field has the parameter 'multiple' set to true automatically by MetaBox, in the file /meta-box/inc/field.php, in the function 'save', the "Save cloned fields as multiple values instead serialized array" block is being called (lines 314-321).
Inside that function, there is a call to $storage->delete( $post_id, $name ).
Now, moving back to the MetaBox Custom Table plugin, in the function /inc/class-rwmb-table-storage.php there is the function "delete" around line 100. Inside, there is an "if" check for "$delete_all || ! $meta_value || $row[ $meta_key ] === $meta_value" and in there there is an assignment: $row[ $meta_key ] = "";
Because of that assignment to "", the function "add" a few lines above fails. Namely, when it calls $this->get( $object_id, $meta_key ) because there is an array conversion happening. The exact line is (array) $this->get( $object_id, $meta_key );
In this case, the "" value gets converted to [""] which is NOT an empty array. All the other values from the text_list get appended and thus the first value is always wrong.
The solution is one of two:
a) in the "delete" function, instead of assigning "", assign an empty array [] if the field accepts multiple entries
b) in the "add" function, rewrite the line $values = (array) $this->get( $object_id, $meta_key ) to:
$values = $this->get( $object_id, $meta_key );
if ( $values === '' ) {
$values = array();
} else {
$values = (array) $values;
}
