From your link:

From the Chicago Sun Times: "Inspectors last saw the explosives in January 2003 when they took an inventory and placed fresh seals on the bunkers, Fleming said. Inspectors visited the site again in March 2003, but didn't view the explosives because the seals were not broken, she said."

The story must have changed slightly because, ABC News leaves out the definitive "seals were not broken statement": "The nuclear agency has no concrete evidence to suggest the seals were broken, Fleming said."

From the Boston Globe: "The explosives that were looted from the Al Qaqaa nuclear facility, apparently in April and May of 2003, had been sealed and monitored by international nuclear inspectors before the invasion." That certainly seems to imply that they went missing in April of May of 2003, before or during the invasion.

The Washington Post writes, "US officials suggested that the munitions may have disappeared before the US-led forces established full control over the country."

The Washington Times cites a Pentagon statement as saying the explosives could have been moved before US troops arrived. "Although some believe the Al Qaqaa facility may have been looted, there is no way to verify this." ... "Another explanation is that regime loyalists or others emptied the facility prior to coalition forces arriving in Baghdad in April."

From the Australian Broadcasting Corporation: "And the US State Department spokesman, Adam Ereli, told us the ordnance went missing before US-led forces had a chance to secure the area."

So, are you clear on it yet? Every single source, except the New York Times, at least mentions that a very real possibility is that they went missing BEFORE the invasion.