Use tsconfig option conflict with compiler project specific.

[Rouche]

The option "use tsconfig" is not saved between restart. TypeScript -> Compiler seems to become checked instead.

It seems like there is a conflict with project specific of TypeScript -> Compiler. When you uncheck it THEN the options disapear and tsconfig option gets saved.
File com.palantir.typescript.prefs

general.useTsConfigFile=true
preferenceStore.tsConfigHash=68047a51190a8552e9ca7a97ae279d540d0b5619
preferenceStore.tsConfigLastModTime=6917389

But after that, the TypeScript -> Compiler option is always checked, even if the options on this page are not.

Weird bug. I will investigate later if it gets too much annoying.