[trng]

Вот так я запускал mxmlc из под air-приложения:

if (NativeProcess.isSupported) {
			var file:File = File.applicationDirectory;
			file = file.resolvePath("file:///C:/Program Files/Adobe/Adobe Flash Builder 4/sdks/4.0.0/bin/mxmlc.exe");
			var args:Vector.<String> = new Vector.<String>();
			var s: String;
			args[0] = "-load-config+=C:/work/Proba/mxmlcconf.xml";
			args[1] = "-define=NAMES::MD5fileName,'"+md5fn+"'";
			args[2] = "-o";
			s = fname+'-pub.swf';
			args[3] = s;
			args[4] = "C:/work/Proba/as3proj.as";
 
			var nativeProcessStartupInfo:NativeProcessStartupInfo = new NativeProcessStartupInfo();
			nativeProcessStartupInfo.arguments = args;
			nativeProcessStartupInfo.executable = file;
 
			nativeProcessStartupInfo.workingDirectory = File.applicationDirectory;
			var process = new NativeProcess();
			process.addEventListener(ProgressEvent.STANDARD_OUTPUT_DATA, onOutputData);
	                process.addEventListener(ProgressEvent.STANDARD_ERROR_DATA, onErrorData);
	                process.addEventListener(NativeProcessExitEvent.EXIT, onExit);
	                process.addEventListener(IOErrorEvent.STANDARD_OUTPUT_IO_ERROR, onIOError);
	                process.addEventListener(IOErrorEvent.STANDARD_ERROR_IO_ERROR, onIOError);
 
			process.start(nativeProcessStartupInfo);
}

Попробуй вместо mxmlc.exe поставить cmd.exe c аргументами:
/c reboot.bat

Должно работать.