For a number of the Analysis functions, DS9 requires temporary disk space to download and store data. By default, this 'temp' directory is defined by the TMP or TEMP environment variable. This is usually defined as /tmp for Linux and MacOSX users. For Windows users, this will vary, depending on which version of Windows you have. In any case, if the temp directory is not writable, or you have specified an invalid directory in the preferences, these functions will fail with a variety of error messages.
Note that if your /tmp directory is mounted -noexec, binary table filtering does not work. Before starting DS9, set the environment variable FILTER_TMPDIR to a directory that is both writable and can execute.
If DS9 fails to start with the following error message:
Application initialization failed: Can't find a usable tk.tcl in the following directories...
It is possible that your system admin stripped the DS9 binary in an attempt to save disk space - but this breaks it (on Unix). DS9 is based on tcl/tk which is a scripting language which requires many support files. To create a stand alone application, we fool tcl/tk into thinking that it has a valid installation. To do this, DS9 is really a chimera of an application and an attached zip archive.. The first thing DS9 does on startup is to create a virtual file system in memory and unpack that archive into memory. The application DS9 is already stripped of debugging symbols when built. The system strip command can remove part of the zip archive, and hence DS9 is unable to un-compress it. In summary, don't strip the DS9 binary and everything works fine.
The DATASEC keyword used in some FITS files specifies what portion of the image is valid data, for calculating min / max and for displaying. This is very important for images created from CCDs with over scan and bias strips. By default, this support is enabled. However, a number of fits images have invalid values for this keyword. Therefor, when DS9 opens the image, it finds no valid data to display - all the user sees is a white image. To correct this problem, either disable DATASEC support, via the Scale menu, or correct the the value of DATASEC in the fits header. You can also change the default behavior by disabling DATASEC from the preferences menu.
The DS9 startup file ds9.ini must not be group/world writeable.