Any advice on a problem with third party source?

I am using libxbee (a lirbary for using the xbee wireless interface) in an application, and it has a bunch of files with the same names, but in different folders. In Visual Studio, it looks like all the obj files are going into one directory, so various obj files are being overwritten by others. Has anyone run into this before? I can solve it within Visual Studio, where I can specify a output folder per source file, and thus put them each in a coresponding subdirectory. But, I can't do this thru the Introjucer. My current solution (hack) was to actually rename the files, but this will cause long term maintenance issues in keeping my source up to date. Thanks for any advice.

Wow, does Visual Studio really not handle that?? Even in newer versions, e.g. vs2013?

I'm using 2008 at the moment, but I'm not stuck on that version (I just haven't wanted to take the time to deal with any upgrade issues). It took me a while to figure out why my builds were acting different with each build. I was really surprised when I figured out why, and even a little suspicious that I must be doing something wrong. But all my tests point to this as the problem. I'm stuck while waiting for some hardware to arrive, so maybe I'll take the time to experiment with a newer version of VS.