So, I transferred PokeRus to my Gardevoir so I could then transfer it to and EV train my Scyther, Lucario, Weavile, and Growlithe. I succeeded and trained my Pokemon, putting them in my PC after I was finished. This was probably a week ago. I was going through my boxes when I noticed that all of the above Pokemon have lost the PokeRus and none of them have the little smiley face icon that appears once it has worn off. However, my Blaziken, which I at some point or another spread the PokeRus to, still has it. Is there some sort of mechanic that I'm unfamiliar with that explains this?

This problem never happened to me when I put PokeRus onto my eevee and then put it in the PC. I simpily think it is a glitch until I am proven wrong (we had the luminose save glitch, any glitch could occur now)
Another possibility is you haven't looked for the pink simile face, or it's a different icon (all my pokemon still have pokerus). Or perhaps pokerus never transferred to your Pokémon. I would say it's a glitch. Mabye they don't show the smiley face anymore? Here's some advice. Use your blaziken to re-infect your pokemon, if they don't get infected, then they have already been infected at some point, and if they get infected, they were not infected.

-Mew77

This has been happening to me too!! It has to be some sort of a glitch because i can reinfect previously infected pokemon the pokerus disappeared from. The only ones that keep it are the ones in my pc. Im not sure but i think instead of the infected pokemon getting the normal smiley when the clock turns over at midnight, it just erases. My Whole party had it, lost it and i infected them again then they lost it... AGAIN. So i infected them and whenever i am going to save and stop playing for a while i have to put them in the pc so that they still have it when i play the next day. So far none has been able to get the purple smiley, it just vanishes. Without a trace. Into the night. Like Batman.