I would not worry at this time, keep an eye on it though.
A short explanation may help here.
First, If you look at your /etc/entropy/repositories.conf file on both machines, you will see that they are different.
The 5.5 machine will be using the standard repo's, while the 6 machine will be using the new weekly repo's.
The way I understand it, the weekly repo's will be updated once a week. I think this is a great idea for stability, the updates would have been in the main repo's for a matter of days, before being added into the weekly repo's.
This would allow the updates to be tested yet again, before hitting the weekly repo's.
I love this idea!
I really do not know much about it, would love to hear lxnay chime in and explain it better.
I do know, with your 5.5 install, it will always use the main repo's, nothing touches those. You would need to change them yourself, if you wanted to.
You also have the opportunity to switch your 6 to the same repo's your 5.5 uses.
Or you could just sit back and enjoy.