CI3 WHERE and ORDER_BY errors

I have been looking into moving my one of my sites from CI2 to 3 and hit a snag that I have been unable to track down.  This code:

PHP Code:

$this->db->start_cache();
$this->db->select( 'molecule.idmolecule,molecule,comment, molecule.projects_id');
 $this->db->where( 'projects_id', $this->project_id );
$this->db->from( 'molecule' );
$this->db->order_by( 'molecule', 'ASC' );
       $query = $this->db->get_compiled_select();
       print_r($query);
$this->db->flush_cache(); 


Returns this query which appears to me to be correct:
SELECT `molecule`.`idmolecule`, `molecule`, `comment`, `molecule`.`projects_id` FROM `molecule` WHERE `projects_id` = 7

If but it also returns this error even when I place a die; immediately after print:


A Database Error Occurred

Error Number: 1054
Unknown column 'projects_id' in 'where clause'

UPDATE `ci_sessions` SET `timestamp` = 1424579236 WHERE `projects_id` = 7 AND `id` = '51ae29260b86c80abe0c60829071d14727c66bdb'

Filename: libraries/Session/drivers/Session_database_driver.php
Line Number: 239

This is coming from both the WHERE and the ORDER_BY lines.  Removing both returns the data I expect.  That 'id' in the database error block is the session id.  Is this a bug or did I miss something???

Edit:
I did not have enough of the code pasted originally. I have traced the WHERE and ORDER_BY problem to having the start_cache and flush_cache lines.