It seems a call to FpgaDownloadAndGo() powers the antenna.

Solution:  Turn off antenna afterwards

armsrc/appmain.c

@@ -1152,7 +1152,9 @@ void  __attribute__((noreturn)) AppMain(void) {
 	// Load the FPGA image, which we have stored in our flash.
 	// (the HF version by default)
 	FpgaDownloadAndGo(FPGA_BITSTREAM_HF);
-
+	// turn off antenna
+	FpgaWriteConfWord(FPGA_MAJOR_MODE_OFF);
+	
 	StartTickCount();