Yes it did.
I took your advice (and the advice of others in RL) and decided to be honest with the travel agent. She was surprisingly receptive and I got to hold the ticket for long enough to submit the visa application properly. In fact I just received the visa back today. Now I just have to wait for the financial aid to start disbursing and then I'll have enough to buy the ticket again.
Though as a side note it was just my (bad) luck that when I went to make the fees payment to Japan that was the other part of my troubles, I found out that the yen-dollar exchange rate was the worst in many, many months and had to shell out more than expected. =_=
Still, it was solved, so thank you. And good luck to your trip as well! Come to think of it, where are you going?