It appears there's more to the story behind the nationwide shortage of Eggo waffles.

Kellogg's has blamed the shortage of its popular breakfast foods on flooding and equipment changes and repairs at the company's bakery in Atlanta, Georgia.

But ConsumerAffairs.com has confirmed the Georgia Department of Agriculture (GDA) in September found Listeria monocytogenes in a sample of Eggo Buttermilk Waffles made at the Atlanta plant. Health officials took the sample during a routine inspection of the facility.

The Centers for Disease Control and Prevention (CDC) says eating foods contaminated with Listeria monocytogenes can cause listeriosis, a serious infection that primarily affects the elderly, pregnant women, newborns, and adults with weakened immune systems.

After the discovery, Kellogg's closed the plant during most September and October to clean and sanitize the facility.

The company also recalled approximately 4,500 cases of its Eggo Cinnamon Toast Waffles and Toaster Swirlz Cinnamon Roll Minis made at the plant. Georgia officials said there are no reports of any illnesses linked to the recalled waffles.

A Kellogg's spokesperson today downplayed the relationship between the Listeria contamination and the current waffle shortage.

"Just as the Atlanta facility was about to resume production, excessive rain in the region caused flooding at the facility which delayed the start up," spokeswoman Kris Charles said in an e-mail sent to ConsumerAffairs.com. "The plant is now operational."

Charles said the company is working "around the clock" to get Eggo waffles back on store shelves. But the waffle shortage, she added, will continue through the first half of 2010.

In the meantime, Charles said Kellogg's will allocate available products to its customers based on an "historical percentage of business."

Consumers with questions or concerns about the waffle shortage can contact Kellogg's at 866-971-3320.