hmm that's weird... the best advice i can give you is to make sure you punish/give him "timeout" or praise him appropriately (this really messed me up at first with my tama, trust me... figuring out just what to do to train him is why i joined tama talk!).
praise/comfort him if he has his back to you or is crying/upset.
you should only punish/give him timeout when he beeps at you but is floating around the screen like normal (assuming of course his hearts aren't all empty!)
if you punish him properly he will cry and whine and will probably have an empty happiness heart for you to fill...
other training: these don't raise your training bars but are fun and interesting...
if you catch your tama right as he's about to "go" (you'll know because of the stink?? lines and that ridiculous look on his face) quickly try to click the toilet icon... and tama will go on the potty! however this does not raise his training bars and can quickly turn frustrating trying to catch him in the act on time!
and before his bed time (arond 20 minutes or less?? maybe even a half-hour, i'm not sure... you'll quickly figure it out), you will notice him "yawning" (it doesn't really look like a yawn, more like the tama burps with a mini "stink" line coming out... heh) and you can turn the light off and he'll go to sleep! again this does not raise your training score but i believe i read somewhere that doing so will fill a happiness heart (hey, if it makes tama happy... whatever!)
i hope i could help as much as some of the folks on the board helped me. :]