Most likely, the agent for the seller knows of issues with the home that would present problems for the FHA appraisal/inspection that would ultimately be performed.
FHA has a set of "minimum" standards that the property must meet to qualify for the financing. If there are any major issues with the property, i.e. structrual, plumbing, etc, etc. the property may not qualify for the financing, potentially killing the deal - or at least forcing the issue to be remedied prior to approval. If the agent knows of these problems in advance, they will simply not accept FHA to avoid the deal falling through as a result of the property not meeting the FHA standards.
Hope this helps!