Menards says the problems began last year when it says the DNR asked the company to build flood retention ponds on the proposed construction site.
Menards says it complied with the request only to have the DNR then claim those same ponds would then dry up wetlands and displace thousands of migratory birds.
Menards says it again redrew its plans, even though according to the company, the area described as wetlands measured less than one acre.
The final meeting, according to Menards, came in November when the DNR said it would deny the company's permit request even though Menards offered to create about two acres of new wetlands to replace the area being filled.
On Monday DNR officials said they weren't sure what application Menards was talking about and they said there would be no comment today.
Local legislators, DNR officials and Menards representatives will meet to discuss the issue in Madison next week.