На машине не пробовал, как без dll будет работать хз, но батником можно одним обойтись 
@echo off
move "c:\Program Files (x86)\Rheingold\TesterGUI\bin\RheingoldFASTA.dll" "c:\Program Files (x86)\Rheingold\TesterGUI\bin\Release\"
move "c:\Program Files (x86)\Rheingold\TesterGUI\bin\RheingoldFASTAConfigParsing.dll" "c:\Program Files (x86)\Rheingold\TesterGUI\bin\Release\"
start /d"c:\Program Files (x86)\Rheingold\TesterGUI\bin\Release\" ISTAGUI.exe
ping -n 30 127.0.0.1 >nul
move "c:\Program Files (x86)\Rheingold\TesterGUI\bin\Release\RheingoldFASTA.dll" "c:\Program Files (x86)\Rheingold\TesterGUI\bin\"
move "c:\Program Files (x86)\Rheingold\TesterGUI\bin\Release\RheingoldFASTAConfigParsing.dll" "c:\Program Files (x86)\Rheingold\TesterGUI\bin\"
exit
Для тех кто растягивает окно используя Launcher http://bmwtools.info...r-okna/?p=15643
@echo off
move "c:\Program Files (x86)\Rheingold\TesterGUI\bin\RheingoldFASTA.dll" "c:\Program Files (x86)\Rheingold\TesterGUI\bin\Release\"
move "c:\Program Files (x86)\Rheingold\TesterGUI\bin\RheingoldFASTAConfigParsing.dll" "c:\Program Files (x86)\Rheingold\TesterGUI\bin\Release\"
start /d"c:\Program Files (x86)\Rheingold\TesterGUI\bin\Release\" Launcher.exe 1
ping -n 30 127.0.0.1 >nul
move "c:\Program Files (x86)\Rheingold\TesterGUI\bin\Release\RheingoldFASTA.dll" "c:\Program Files (x86)\Rheingold\TesterGUI\bin\"
move "c:\Program Files (x86)\Rheingold\TesterGUI\bin\Release\RheingoldFASTAConfigParsing.dll" "c:\Program Files (x86)\Rheingold\TesterGUI\bin\"
exit
ping -n 30 127.0.0.1 >nul
30 это задержка в секундах для тех у кого компы послабее и не успевает стартануть время можно увеличить.
Ну и проверить путь где у вас установлена прога 