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[postdoconsteroids]

Is it appropriate to contact the departmental secretary or other individual tasked with receiving applications for confirmation of receipt?

I know that contacting the SC is a non-starter. 

But I am concerned, as my post office has lost or misplaced several items I've mailed within the last few months.

[spectacle]

I would leave it alone. 

To me, the only thing worse than irritating a SC is irritating a department secretary.

If you're that concerned, in the future send things with delivery confirmation.

[anisogamy]

I wouldn't do it either.  Sorry, but I think this is one of those things where you just have to hope that everything went as it should have (and possibly get delivery confirmation next time).

[seniorscholar]

I think that it would be acceptable to contact the department's admin asst (who probably doesn't handle applications if it's a big department, but can easily pass the request along to the clarical worker who does) only if you are not in the same country as the university to which you're applying. Yes, I know the US post office loses mail going to the US (and only last month it took four days -- without a weekend -- to receive a prescription mailed by my doctor and postmarked in the same zip code as mine), but I think the department's staff would probably be forgiving rather than annoyed if someone lives across a border or an ocean.