If you are not running the CH Control Manager, the only way the game could lose its link with the stick would be if the USB bus is resetting. However, it would lose all the settings, in that event.
The situation you describe, which seems to be continuing to happen over and over again, suggests there is something wrong with either the operating system (it keep putting the USB bus to sleep and not waking it up properly, a known problem), or the stick itself is having issues.
I have asked several times, and I will ask again.
What commands are mapped to the axises which are not working?