I run into the same problem quite a bit. In the first hour of an online MTT, I am often able to steadily build my stack. By that I mean, starting with 3000 chips and hitting the first break with 6-7K, give or take.
In the 2nd hour, the short-stacks are the biggest menace for me - or the guys that buy in at the first break. These guys are desperate to double up and have opened up their range - shoving with any Ace, any pair, any suited face cards, etc. If I'm card-dead, it's foolish to try to outdraw them. One wrong move and I'm the guy shoving KJ.
Of course, there are times when I'll have hands/situations where I can call the short-stack. When it goes my way, even just one time, I can usually make a good run. If I survive the flurry of short-stack shoves in the 2nd hour of online tournament, I feel very good about my chances for cashing.