Have you checked Options --> MIDI --> Notes Transposition (at the bottom of the MIDI pane)?

A few times, because of some anomalies, inconsistencies or problems with the various apps and devices the sound is routed from, to and through, the frequency changes. Sometimes it seems like a mismatch in samples per second is involved (like 48000 sps being played back at 44100).

Linux has several competing sound systems/routing (PulseAudio, ALSA and JACK), so their interactions sometimes cause audio "weirdness."

That settings is zero in both standalone and vst-plugin. I'm on windows 10 and using ASIO, but you're right - the settings do weird things! I switched the soundcards ASIO panel settings from 24 bit to 16 bit and it's in tune again

A few times, because of some anomalies, inconsistencies or problems with the various apps and devices the sound is routed from, to and through, the frequency changes. Sometimes it seems like a mismatch in samples per second is involved (like 48000 sps being played back at 44100).

Linux has several competing sound systems/routing (PulseAudio, ALSA and JACK), so their interactions sometimes cause audio "weirdness."

It's quite noticeable, almost a whole note down. The UI still shows the correct key that I press on the midi keyboard - just the sound is off. It's like someone is holding the pitch wheel, but I checked with midi ox, that it's not sending any wrong midi signals - also it still works whole way up and down.

For some reason if I use programs like VSTHost (vst2 or vst3 plugins), it works fine. The problem is with the standalone.