Do you have the program set to open on startup? I know hibernate mode can be a little finicky on windows, does it act the same if you sleep/wake up your PC?
As for the entries being automatically deleted, do you mean in the faders section to control audio levels? I have to do the same whenever my Discord or Spotify update. They become faded out (signifying that the EXE was not found) and I click the drop down and select the new EXE and remove the old one.
(I wish there was some automatic search function when the specified EXE was not found, for programs that update and rename itself eg. with a build number)
For the hud not being the same as the name of the program, do you keep the old (faded out) app on there? It may be saying "more than 1 program found, defaulting to fader name". It does sometimes glitch and show the fader name when there's only one program on it, but for me it usually resolves itself in a few minutes iirc. Alternatively, you could try restarting the program to fix the instance of the glitch, it will most likely happen in the future.