I experienced the same. That’s why the idea to put modifiers as dual use keys on the home row doesn’t work out. No matter how hard I trained to improve my accuracy, I always ended up with several keys being active at the same time, causing strange undesired short cuts being emitted.
As we are talking about timing. @algernon: Have you ever measured the time it takes to process keystrokes when using different plugins or combinations of them. Are there combinations that limit typing speed due to excessive processing or is the atmega always fast enough?