After trying to embedded my projects dependencies with ILMerge first and Fody/Costura, I am facing the same problem with both.
The titlebar height seems to shrink. The VS2015 debug binary and release binary (without embedding dependencies) has the proper height and padding (as you can see on the screenshot). Including an icon doesn't solve the problem unfortunately. Do I have to include something additional in the Costura XML?
What am I missing?
.NET Framework 4.6
EDIT:
Apparently my issue was due to using FixedDialog as FormBorderStyle. With any fixed style the padding would vanish after embedding the dependencies. But it works perfectly fine with Sizeable (Default) as FormBorderStyle.