A dot in the URL defines an extension, as defined in the RFC's.
So officially you should encode data that has a dot in it. Alternativly, you can disable striping the extension in the routing section of the config.php (1.4+).
Or you can use the Input class to fetch the stripped extension, and stick it back on your parameter once you have retrieved in it your controller method.
A bit of a hack, but a solution if you don't want to disable striping extensions for all URI's.