I read your question several times to make sure I am following you correctly.
What I am perceiving from what you are describing is that you are attempting to put two files of the same name in the same folder at the same time. Is this correct?
Normally it will create or allow the file to be in the same folder but will add a 2 to the end of the file.
such as bla.exe and bla(2).exe
I use Microsofts Visual Studio 2010 a lot and have created batch files for some programs I have worked on and only use Windows 7 most of the time.
I have not experienced the issues you speak of with being warned that the batch file is in use elsewhere on my system when I am working with a batch file.
If I am way off course here, sorry about my misunderstanding your question.
Edited by MrBruce1959, 16 December 2010 - 02:08 AM.