96 geo tracker knocks 1-3 gears and quiet in 4th and 5th

I have a '96 Geo Tracker and it runs great BUT when starting out and shifting to second then third it knocks like a rod went out in the motor, but when shifted to fourth or fifth it is fine. Does anyone have any insight on what the *#^@ is going on? The clutch does not slip either and the transmission was replaced last year. I know it is not the motor but have not looked into anything as of yet. Just thought I would get some ideas before I start snooping around and probably break stuff!!

Might check valve clearances etc - recommended every 15000 miles. Also if it is a manual, check clutch cable - it can cause some funky stuff - and they last about 2 years if you drive the vehicle. Some times a rod will be noisy at rpm and load rpm combinations. But it sounds like something loose in the trans - maybe a cracked ring gear only used in those ranges.