NIOSII Syntax on Quartus 13

I am having a problem verilog syntax NIOS suggest for exporting the signals into Quartus for version 13.

In some cases it suggest to use '.bidir_port_to_and_from_the_sys_scl' and in some other cases it '.sys_scl_export'. This is obviously not for the same signal.

In some cases I notice that this, what I call syntax discrepancy, is messing with the functionality of the signals.

Is this a problem? How can I fix it?