C:\Program Files (x86)\Microsoft SDKs\TypeScript\1.0\tsc.exe
C:\Program Files (x86)\Microsoft SDKs\TypeScript\1.0\tsc.js
for some reason the typescript was installed separately (not via npm) there, and that exe file replaced new one from npm.
removed that folder (“C:\Program Files (x86)\Microsoft SDKs\TypeScript”) and problem was fixed.