I went to Halifax Consulate in Canada to change my F-1 VISA to J-1 in December 2003. Although my VISA application was immediately approved by the Consulate General, I had to wait to get a security clearence from US State department. I was told by the Consulate General to wait until I got the secutiry clearence. They couldn't tell me how long I had to wait. After calling the US-VISA helpline in Washington DC, I was told that security clearence can take from 2 months to 18 months and each case is handled differently. Since my F-1 VISA was already expired, I couldn't travel back into US. According to the new VISA regulations, one must possess a valid VISA to re-enter US.
After 43 days, I was called back to the Halifax consulate to get my VISA.
Even though I was a student in US for 6 years and was already in a post doctoral position for almost a year at a US Federal Government research institute, I had to wait for a month and half to get the security clearence.
I would advise others in similar situations to read all the bulletin board messages on the US immigration web sites and also the warnings posted on the individual US consulate websites before making travel plans outside USA.
When I went to mumbai consulate for the first time for F1, I got rejection. And in second effort the officer asked me almost same questions with very little change and I was granted VISA. SO DONT GET NERVOUS IF YOU ARE REJECTED ONCE.
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