iControl, bigip.conf possible descrepancy?

Update. Did more testing. Found that after I ran an iControl config save, I'm still seeing the same behavior as is described in the original post ( pool definition is missing an association in the bigip.conf file that exists in the GUI! ) I think the config save works because I see the bigip.conf and other conf timestamps being update. Is this the correct method to save the configuration?

my $ConfigSync = SOAP::Lite
-> uri('urn:iControl:System/ConfigSync')
-> readable(1)
-> proxy("https://$f5_ip/iControl/iControlPortal.cgi"); 

my $soapResponse = $ConfigSync->save_configuration
(
SOAP::Data->name(filename => 'full' ),
SOAP::Data->name(save_flag => 'SAVE_FULL' )
);