Transmission or Ecu problem?

I have a 2000 toyota sienna xle. I purchased it brand new from the dealer in 2000. So far it has all routine oil changes and mantinence. Lately the transmission has been jumping when shifting from 1st to second gear. Its an automatic and the car only has 64 thousand miles on it. I took it to a repair shop and they told me that the transmission was not the problem but the ecu. They did a transmission oil change hoping to find a bolt or something but there was nothing. It started happening when i installed a new battery. Does any one know or think that the ecu is the problem? they say it reset. please help. Iv'e already paid 1000 dollars in repairs and diagnostics.