replaced transmission on 99 V6, now making a whining sound.......

Hello, I have a '99 V-6 with auto trans. Last week the check engine light went on. My mechanic got the code and said it was the trans. solenoid or the torque converter. So, I took it to the Honda dealer. They said it needed a transmission. I have an extended warranty on the car, so I said go ahead.
 
I got car back tonight, with the new trans, and I drove about 5 miles at speeds under 40 mph. I pulled into a shopping center, and I noticed a faint whining sound coming from the firewall. I put the car in park and it went away. I turned the car off. Then a little while later, I restarted the car and put the trans in gear and the whining started again. I drove the 2 miles back to my house and I was noticing that it was intermittenly doing this whining the whole way back. It is sort of like a bearing whine, but its hard to tell.
 
Is there any break in time on trans? By the way, this is a Honda re-manufactured unit with a 3 year 36K warranty.
 
Please let me know what you think, as I want to take it back to them tommorow and get it checked out.
 
 

yes, there is a break in time... actually miles... 500 i believe....