roseml, you're the 700 vs 26 person South America right? If you do your trip and end up in Central America, you will be an expert on border crossings by then, don't worry.
-For me, nothing major, just surprise "exit" fees that are not ever clear if official or not (Mexico into Guatemala)
-some Nicaraguan exit fee guys who were purposely slow on giving change to the U.S currency fee only exit fee, combined with trying a "you only gave us a $10 and not a $20" trick on for size, combined with the fee supposedly being $12 but the receipt finally given after a long wait and out of the side door of the bldg was for $2.
-the usual money changer guys and ladies who crowd you and stand too close to you to see into your bags and what passport you own
-at busy borders, often its not clear of where to go and what to do, just a lot more people around, and the odd dodgy fellow who you should keep an eye on your bike. ie simply turn your suspicious radar up and be extra aware of your belongings.