ipod touch over capacity

Recently and only sometimes my ipod touch 3rd Generation states it is over capacity. I know there is approx 5.9gb free.
It started when the new version of itunes was updated - latest version done last week.
Some over capacity starts when the ipod syncs and then it sometimes disappears and shows me the correct capacity. But at first following the new download version of itunes it stayed as over capacity of 1.3gb.
Can someone please explain why I get this? Should I be concerned about it happening each time I plug in the ipod and it starts syncing.
I know there is free capacity.
Thanks