The first issue sounds like it's down to trailing slash (either one that's omitted when it's expected, or expected and been omitted). If you send me the relevant parts of your Apache config I'll take a look.
The %2f problem is down to a change in a very recent version of Template Toolkit. The 'uri' filter now considers '/' to be characters that it should encode, which it does, resulting in %2f in the output.
Right now, your choices are either:
a) Downgrade the TT installation. Version 2.15 is known to work.
b) Adjust the templates. If you haven't changed anything, look in the templates/trac directory of the directory in which you ran svnweb-install.
It's probably sufficient to find everything that looks like this:
... /ACTION[% c.path | uri | html %]...
(where ACTION is one of the actions, like 'log', 'browse', 'view', and so on) and insert a slash straight after the ACTION, so that it becomes:
... /ACTION/[% c.path | uri | html %]
I haven't had the chance to test this though.
If you do (b), and it works, please let me know (nik@ngo.org.uk, or svnweb@ngo.org.uk for the mailing list) and I'll roll that in to a new release.
I will be looking at this, but I don't have a great deal of spare time at the moment. It's top of my list of things to resolve though.