answers here...

You were supposed to pay for $1000 in 2004 before the reinstatement of $1500 or $750. Of course you did not pay for it. Now when they review your extension, they found out you did not pay before and ask you to repay $750 or $1500 (if company size larger than 25).

Exempt H1B nonimmigrant includes 1) those with a salary higher than $60K 2) or with a Master degree or higher education.
It's not related to training fee.