Sounds like a couple of things got mixed up in the translation...
You are paid an "expense reimbursement" check of $400/wk for the first month as a new hire. These checks are "tax free". The company files the expense reports, you do nothing. Starting on your 5th wk of training, you are your monthly guarantee (pay period is twice a month) of 75hrs/month at first yr pay. Taxed normally.
The $5000 bonus is paid in 2 installments, one after wk 2 and the other after wk 4. This is taxed. In accordance with federal tax laws, since these checks are so "large" they are taxed at a higher rate which you will get back next yr when you file your taxes.
So first 4 wks of "pay" is not taxed, signing bonus is taxed.
Hope this helps.