On my Silver version, back before I restarted my game, I'd noticed something weird. When my Typhlosion reached level 85 or so, when I would take him out of the PC, it's cry would be delayed. I'd hit "Withdraw", and it would wait about 3-4 seconds, and then I'd hear it. None of my other Pokemon waited that long to cry. Did anyone else have this happen on their games when they withdrew high leveled Pokemon, or was it just a glitch? I'd never heard about this happening before.

This is normal, not a bug.
When you withdraw a high level Pokemon from the PC, it takes a long time to withdraw. (I have to wait TEN seconds before I withdraw a lvl 100). So there's nothing wrong with your game, it just takes a long time to transfer that much memory.
- DNA

Yeah that bugs me, It really slows me down when duplicating stuff

Oh good, I thought my game was messed up or something, which is part of the reason why I deleted that save file and started new. I feel dumb now...