If it's one of your primary tools of navigating code without using the mouse, it's going to be a concern.

For example, in Visual Studio ctrl-x with nothing selected will cut the whole line, but very few other programs support that. As well as using to move code around, I use it to delete lines (ctrl-l is better supported, but you can still do ctrl-x with your hand on the mouse). So when it doesn't work in Notepad++, it's quite annoying as it breaks your flow. I'm using a plugin to simulate it, but it's not quite right still.

One of the another thing that can catch you out is that the various MS code editors behave differently depending on the language you're using, SQL Management Studio will treat anything wrapped with []s as a single string, but while in text strings of SQL in Visual Studio it will stop on each bracket. It end up being quite annoying you can't mark a string in VS as a sql string when you want to make a small tweak or add an extra column.

It's muscle memory, and so it's going to annoy you when it doesn't work, it makes you feel clumsy in the new environment.