There is a high chance that any insertional line carries more that one T-DNA inserted in the genome. In fact, as long as I remember from the Alonso et al., paper on Science about the Salk collection, the claim that 50% of the lines are supposed to carry 2 or more T-DNA inserted in the genome. Try to analyze more seedlings or an allelic line for that gene.
Gabriel León, PhD
Center of Plant Biotechnology
Faculty of Biological Sciences
Universidad Andrés Bello | República 217 | 1 piso
Santiago - CHILE
Oficce: +56-2-770 30 35 | Lab: +56-2-770 30 34