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So in order to get a working chat in Red Dead Redemption Online i installed mIRC but it doesn't work when putting it on top. But it works on the PC of my wife for some reason, any ideas?
The mouse realizes the window is there tho, as it changes and i can click the windows, cicking me to the desktop.

If you enable the "on top" feature, does it work correctly on the Windows desktop? ie. Is it correctly positioned over other normal windowed applications? If it is, then that means it is working. However, as any application can use this setting, if multiple applications use the "on top" settings for their windows, they will compete for the "on top" position, and there is no guarantee which one will actually be on top. From your description, it sounds like mIRC is on top (because the mouse is reacting to it) but the game is drawing over mIRC. I am not sure how you would get around that.

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And the second question: tried to make the window transparent but failed miserably.

Windows only supports transparency on top level windows. This means that you would need to have your status/query/channel/etc. windows open as desktop windows by default. This can be enabled in the Options/Display/Options/Windows dialog. If you make this change, are your windows transparent on the windows desktop? If they are, then the feature is working. However, transparency depends on Windows to manage and blend all of the currently displayed Windows. In addition, some Windows features can disable transparency, eg. if you use "basic" or "classic" theme on Windows 7. Windows 10 handles this much better.

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Preferably without menu or borders.

mIRC does not support removing titlebars, menus, or borders from its standard windows.