The first thing I did after installing 4.3 was to download and read the updated manuals.  I assume Captain Sim 2 is referring to this section of Flight Manual Part II:

Quote

IRS Alignment
An IRS must be aligned before it can enter NAV mode. Rotating the IRS mode selector from OFF to NAV begins the IRS alignment. The IRS performs a short power test, during which the ON DC light illuminates. When the ON DC extinguishes the ALIGN light illuminates. Alignment requires approximately 5 minutes.
Present position (latitude and longitude) must be entered on the CDU position initialization page to complete the alignment. If the present position cannot be entered through CDU, it may be entered through the IRS mode selector keyboard.
If the latitude/longitude position is not near the original airport, the CDU scratchpad message VERIFY POSITION is displayed. If the entered latitude/longitude position does not pass the IRS internal comparison test, the scratchpad message ENTER IRS POSITION is displayed.
Alignment can be accomplished only when the airplane is parked. Alignment stops if an IRU detects motion during alignment. When the motion stops, some units restart the alignment automatically.
The IRS is aligned when all IRUs enter the navigation mode.

Unquote

I understand the first sentence to mean that the IRS mode selector knobs are switched from off directly to NAV, not to ALIGN.  When I do this, the ALIGNMENT indicator lights (3) come on steady, then extinguish, and after about 30 seconds all 3 indicator lights begin to flash.  At this point I open the CDU and input the lat/long for present position in the scratch pad and then enter the data into the boxes using the switch to the left of the boxes.  The ALIGNMENT indicator lights extinguish.  I go through the rest of the preflight settings in the CDU and other panels, taxi and take off.  The Present Position shown on the IRS never changes from the present position entered during preflight and alignment.  I have performed the above procedures with engines running and with engines shut down, the results are the same either way.

Am I misunderstanding any part of the procedures stated in the manual?