Your first problem was naming the machines the same... once you do that, Time Machine used that name to identify the host(s) when they were backed up. Changing it later obviously wouldn't change Time Machine's idea of the host's name.
Have you tried using the Time Machine System Preferences pane, disassociating the backup volume and re-assigning it?
I'm actually surprised by this. I would think that Time Machine would associate something more unique to the machine, rather than a name given by the user. I was about to name my new MBP the same name as my previous one, after I reformatted and gave away my old one, but decided to put the year in the name, thinking that it might be a problem with TM. I'm glad I did.