The only issue would be if you run a newer version of a program that updates it'...

pyre on April 29, 2011 | parent | context | favorite | on: Ubuntu 11.04 (Natty Narwhal)

The only issue would be if you run a newer version of a program that updates it's config file (or something similar) format, which ruins things when you boot back into an older partition running a prior version of the program.