Since WMV belongs to Microsoft, try their software
The above links are outdated since in 2010 the only encoder now provided by Microsoft is Expression Encoder 4, and the free version only exports VC-1 files. If you pay $49 to buy Expression Encoder 4 Pro it will convert WMV to H.264 which is natively supported in IE9. Microsoft Expression Encoder doesn't output to Flash. More info at http://www.microsoft.com/expression/products/EncoderPro_Overview.aspx
I always convert any WMV's to something that PrPro can easily handle. That does NOT restore the lost quality in the WMV compression, but makes life a lot easier, if one has to edit that streaming, delivery-only format.
Try taking the wmvs into a timeline then export to AME from there.