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Many people have reported that on Windows Vista (but not Windows 7), after the Windows security update KB3057839 (part of the update MS15-061 published on 9 June 2015), the PuTTY configuration window does not display. Only a taskbar icon is present. Reportedly, keyboard input and even blind clicking on the invisible configuration window still works. (Some public reports: one, two, three.)
We haven't worked out the root cause of this so that we can fix it properly. We have managed to reproduce it on a fresh Vista installation (it was necessary to switch colour scheme from 'Vista Basic' to 'Vista Aero' to reproduce the symptom).
We've tried asking on Microsoft's forum; this has yielded another program (dBpoweramp) suffering from what sounds like the same symptom.
The PuTTY terminal window works when launched from the command line (putty -load sessionname, putty -ssh hostname.full.domain -l username). Other PuTTY suite programs such as PuTTYgen work.
Uninstalling the KB3057839 update is reported to restore PuTTY to a working state; however, since that's a security update, that's not an ideal solution. (One correspondent reported that uninstalling KB3058515 also worked.)
One correspondent's experience suggests that the window is present but invisible (transparent); they've also posted publicly. They can restore visibility with an AutoHotKey script containing the following:
WinWait, PuTTY Configuration WinSet, Transparent, 255
It's also been reported that hiding and showing the window with ShowWindow() (by hacking the PuTTY source, or externally from PowerShell) makes the window reappear.
Another perturbation that makes the symptom go away is mucking around with SetWindowLong(). It's not clear why, but it has made us a bit suspicious of our use of that family of functions.
Another correspondent reports that setting the Windows properties 'Disable desktop composition' or 'Run in 256 colors' on putty.exe (in the Compatibility tab of the file properties?) avoids the issue. Others report that disabling desktop effects entirely (by selecting the "Windows Vista Basic" colour scheme) also works, although that's a sledgehammer to crack a nut. Presumably all these methods work by removing the possibility of transparency.
None of PuTTY's settings appear to have any effect on this behaviour (which is as you'd expect, since the configuration dialog is itself not configurable); at least, many people have tried erasing their saved sessions, uninstalling, using -cleanup etc with no improvement.
Audit trail for this artifact.