You definitely should charge more for the more difficult searches or extra's.
I no longer go out to the counties and do searches, however the guys who do my work will call me if a search is going to require more time and effort to do, and then I call my client.
In fact it happened today on a search in NJ. Client ordered a 2 owner and we ended up having to do a 3 owner as the prior owner was a bank, I called her and she said no problem.
We are in business to make money and your 2 examples say it all.
Any way, thats my 2 cents.