I also had this problem with a freshly created fedora 25 VM. I am
keeping both cygwin and the VMs up to date.
XWin.0.log attached.

On Tue, Feb 14, 2017 at 3:07 PM, Jon Turney <jon.turney@dronecode.org.uk> wrote:
> On 11/02/2017 22:14, Gulliver Smith wrote:
>>
>> I don't know if this is a Fedora 25 question or a cygwin X question
>> since I upgraded at the same time.
>>
>> Ever since my Fedora 25 upgrade, the menus from programs running on
>> the Linux box using cygwin x as the X server appear off screen at the
>> top left. It is impossible to use these menus.
>
>
> Thanks for reporting this.
>
> There have been a few other similar reports, so I'd like to understand what
> the problem is here.
>
> For future issues, can I ask you to use the cygwin list, per [1]
>
> [1] https://cygwin.com/ml/cygwin-xfree-announce/2015-03/msg00001.html
>
>> An example is Firefox'smenu, but this happens with many Linux programs.
>>
>> Is there a configuration option that I am missing in cygwin X?
>
>
> No, I think this is probably a bug, somewhere.
>
>> Fedora release 25 (Twenty Five)
>
>
> I built an x64 Fedora 25 VM and attempted to reproduce this problem, but
> with no success.
>
> Are you using a non-default visual theme?
>
> Can you attach an XWin.0.log file? I'm interested if you have a single or
> multiple monitor setup, and what the monitor geometry is.
>
> --
> Jon Turney
> Volunteer Cygwin/X X Server maintainer