I think the most direct answer would be
Is there some kind of patch I can download?
No. See below.
The updates don't seem to work when I startup the software.
Can you elaborate?
Is there a newer version of the software I could use? Please let me know how to fix the problem.
Yes. http://bruceravel.github.io/demeter/ You may have seen this link at the top of http://cars9.uchicago.edu/ifeffit/Downloads right above where it says the older versions are no longer supported. --Matt In more detail on why the first answer is "No", I am perfectly willing to take full responsibility. The underlying analysis engine for Athena (Ifeffit) was written in Fortran, mostly between 1998 and 2001. At that time, using Fortran was expedient and the alternatives all had significant disadvantages (taken much more time to develop, been less portable, been non-free, and so on). One consequence of using Fortran was that the graphics libraries were very limited. The PGPLOT library was the best candidate. This was due in part to the fact that it could be run on Windows. So, the fact that you have a window with a plot AT ALL is really based on those software choices. And, in fairness, scientific software written before 2005 all tends to have mediocre graphics. It turns out that the last significant change to the PGPLOT library was in the mid 1990s and the last change at all is from 2001. The library does not allow for communication between the underlying program and the graphics window when you click the X. On Linux/Mac, the user is not allowed to close this window. On Windows, there is no way to prevent the user from doing that, and there is no way to detect this has happened. So, not clicking that button really was the best answer. Now the answer is "do not click that button OR use Demeter". Hopefully, "OR use Larch" is a reasonable answer too. An additional "OR" in that answer is "help us make the software better", by actually helping write this stuff. This gives you many choices: a) use the older, well-used, but no longer supported for bug fixes Athena / Ifeffit code. Don't click the X, don't expect support. b) use Demeter, which fully replaces Athena/Artemis, mostly using the Ifeffit library (still in Fortran). c) use Larch, which fully replaces Ifeffit, but does not give pre-packaged GUIs (for EXAFS, ..., yet). d) help us write the software. Clearly, a) is your worst option. Option b) will probably get you going on your immediate problem in the least amount of time. Option d) is, by far, the best option. Some of you may think I am joking, but I am not. If you think that option is unreasonable, please use the oldest version of Athena you can find.