Check the axle shafts/ the boot may be still intact, but I've seen the outer joint, or inner for that matter, still be bad and it causes noise when a load is on the engine (ex. accelerating or decelerating)
I bought my Hyundai Accent in 2002,I am the original owner. My first transmission went out at 82,000 miles. It was replaced with a rebuilt one, and then 1 1/2 yrs later in 2008 it went out. That was March of last year. Well now it is September 2009 and it has went out yet again. I am starting to realize that there is a manufacturer's defect in this. I am looking into what legal route I can take against Hyundai. Sure the car was cheap, but that does not make it right that there is obviously a problem with the transmission.
You may have a less than competent mechanic who doesn't flush out the trans cooler after he/she installs the new transmission.
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