If you've been logged out for a long time (12 hours?) you get the benefit of a full rest when you log in, including max HP and clickies recharged, etc, which occurs after all stat calculations.
If you've been logged out for less time than that, you're supposed to have the same hp as when you logged out. But, at some point the game changed the order of calculations so it determines your modified Max HP after it sets your current HP, which results in truncation.
It does the same thing with SP, btw.
They just need to make it so setting your current HP/SP is the last thing that happens after logging in again (well, last thing before full rest is applied when applicable).