Has provado trantando de agregar el evento el RowCreated del grid.
Tambien puedes recuperar el valor de la fila sin javascript,
Código ASP:
Ver originalDim gvfls As GridView = DirectCast(Flm.FindControl("gvwFiles"), GridView)
Dim items As New List(Of String)()
For Each row As GridViewRow In gvfls.Rows
If row.RowType = DataControlRowType.DataRow Then
Dim cb As CheckBox = DirectCast(row.FindControl("gvchkFile"), CheckBox)
If cb.Checked Then
'codigo
End If
End If
Next