I thought I'd add my observations as someone who has only been around here for about six months, and has investigated this anomaly a little on my own.
For one thing, I've never experienced a "ghost crypto" occurrence while I was not active on the site. Perhaps this is unique to me, but I wouldn't worry too much about ghosts showing up while you're not here.
Secondly, while the frequency of they show up may somehow be related to internet connectivity, I have seen ghosts occur even at times when I would describe my connection as perfect.
Lastly, as of yet, I have not found any relationship between the circumstances that trigger a ghost. Obviously, it's difficult to nail down exact circumstances since one is not immediately aware of a ghost's existence. One idea I have, is that it is caused by something on cryptograms.org's end, that we all experience if we happen to be playing at the time, but we'd need the admin to comb through the data to prove it, and it still wouldn't solve the problem.
The bottom line is that if you check your Recent Games link every two hours while you're playing and before you log off, you should be able to bust all of your ghosts and keep your 100% record.