(Video in Spanish with English subtitles)
This video will give you a taste of what it is like to deal with the Honduran government. Hee-larious! I'm not sure what country this is from, but while this has a happy ending (oops, I shouldn't have given it away), these guys were wusses compared to Honduras.
In the end, no matter how many hoops you've jumped through, no matter how well prepared you are, no matter how much time you've allotted to your tramite, they always have the trump card (the system is down, come back mañana; we are out of paper, come back mañana; the only person in the entire world who is authorized to sign your document is a) in San Pedro (substitute any city you are not currently in), b) out to lunch, or c) on vacation, come back next week.
I have to say that I've experienced that look of disappointment and even annoyance when I've arrived at the window with all my paperwork in order. Even worse, don't dare to bring something to read while you are waiting — it's highly frowned upon.
Just expect it and get used to it. You have no control over it. ;-)