I went to Nepal this winter and renewed my visa. they did not ask many things so I find it kinda weird that they gave u hard time. anyway it doesn't mean end of the world. you should definitely reapply (no doubt about that). contact your university international office and seek for their suggestions, contact your PI and ask if he can send a letter or something. And I think the important part is to go through your documents and minimize things that shows your intention of staying in US, and put more documents that shows your tie in Nepal. I would remove things like proof of personal property in US and stuff like that, and put documents of your property in Nepal and other documents of relationship and others to show that u have some financial and personal tie in Nepal so you will come back here. don't hesitate to state that you have no intention of staying in US after graduation (its not like they'll come find u after your graduation).

I hope that helps.. good luck man.