These guys are crooks. We booked bus transportation with them from Flores back to Guatemala City. They have a back room at their office in Flores where they encourage tourists to leave their luggage while touring the town and waiting for transportation. We did see that several people had left their luggage in the room so we did as well. However, we had a bad vibe about the "staff"—mostly rough-looking dudes—so we first transferred all valuables to our backpacks which we took with us while walking around town. We had one painting by a Mayan artist worth $800 Quetzales ($100 US) which we left in the room with our luggage because it would have been inconvenient to carry around town. When we returned to their office to meet our bus, the painting was gone. The "staff," rather poorly, pretended they didn't know what happened or how it disappeared. After searching around the back room more than they hoped we would, we found the tubing that held the painting ripped open and shoved under a mattress with the painting still inside. We assume they either had hoped that they would have found something more valuable within and decided to discard it to hide that they had ripped it open or that they planned to sell it later.
Lastly, prior to our leaving in one of their shuttles to the bus station, they also doctored (white out) the travel voucher they gave to us (and did the same to another couple) to put us on a cheaper, more dilapidated bus than the first-class bus for which we had paid them. All they did was change the departure time from 9PM to 8:30PM, which neither we nor the other couple noticed until we arrived at the Flores bus station, and they made a killing by putting us on a bus much cheaper (and dangerous) than that for which we paid. By the time we noticed they doctored the vouchers, it was too late for us to make a change or go back and confront the agency.
Note: these guys pick tourists off at the bus terminal at Flores in the middle of the night when people are confused and disoriented after traveling on the over-night buses from Guatemala City. They stand right outside the bus door as tourists deboard and, in perfect English, offer rides to Tikal. Advice: if you take an overnight bus to Flores from Guatemala City—slow down when you arrive, find the terminal (if one exists-we didn't see one), and do not let these guys fast-talk you into a ride. Ask around for different options or arrange with your hotel in Flores beforehand to have a shuttle pick you up and take you directly to your hotel. These guys want, more than anything, to get you into their offices, find out everything about your trip and what you might need so they can run scams on you.
The lead guy is a short, overweight, dark-complectid man, who speaks perfect English, and looks almost Hawaiian. If he approaches you, stay away from him. I didn't trust him the minute I met him at the terminal in Flores, but we were disoriented and desperate and that state is what they prey on. The arrival point at Flores is chaotic and disorganized, making it a perfect place at which to take advantage of tourists.
Book all transport through your hotel and ask your hotel who they use. Make all arrival and departure reservations before leaving for Flores. Do not wait until you are in Flores to book your return travel. Either book it in Antugua or in whatever other city you find yourself. Book as little as possible while in Flores. Get as much done as possible before you arrive.
San Juan also goes by the name Maya Expeditions. They may run the entire town and you may have few options, but if you see either of these names, do all you can to avoid them.