hmm... I don't think its the "steam getting inside the box" that kills bacteria persay, but rather the high temps/pressure. Regardless if the steam gets in, the high temps/pressure will purge those bacteria.
Here's a little thing you can do though. Take a piece of autoclave tape (normally no black lines; turns into black stripes at high temp/pressure) and put it inside your tip box. After that, autoclave your tips, then bring your tips somewhere sterile like a culture hood I guess and check if that tape changed color to soothe your worries. If it did, your samples are sterile. Congratulations!
I'm no expert on this so someone correct me before poor OP has crap growing in his cultures. 🙂
edit: OP if your lab has preracked tips those are sold sterile (RNase/DNase free) and will remain so if you are careful and use them under sterile conditions.