There seem to be a confusion about the Jordan on arrival visa for Indian passport holders. This post is targeted to clarify that.
I recently flew through Amman's QA Intl Airport. After landing, I approached the visa counter (not the transit counter), and got an on-arrival visa stamp in exchange of 20 JDs, without any problem. They did not ask anything, and gave the visa right away. Note that, however, some people like flight representatives on the airport had told me otherwise. I suggest to ignore them and directly approach the visa counters.
If you're traveling through Royal Jordanian and are only making a transit stop, make sure you also collect the free hotel ticket from the ground staff.