Keyboard handling is broken with .Xmodmap config

I use .Xmodmap config on Linux to replace 'Ctrl' button with 'Alt' button.
Here is it:

clear control
clear mod1

keycode 64 = Control_L
keycode 37 = Alt_L

add control = Control_L Control_R
add mod1 = Alt_L 

I use it for a long time and everything work fine. But Qt Creator > 3 builded with Qt5 works strangely.
Actually Qt Creator detects new key map and old one.
For example:
I want to copy-paste something. I press Alt(which is mapped to Ctrl)+C and selected text copied to buffer but also menu bar is activated. So if I press 'F' button after it - File menu will be opened.

Basically it makes Qt Creator hotkeys unusable. And hence, Qt Creator.

This bug appears only in Qt Creator >3.0