When changing the directories for downloads and partials, it will accept input of any directory, but the change will not actually take effect if the directory contains characters like '.' or '-'.
It also does not seem to accept anything for the 'partials' directory if it exists within the directory specified for 'downloads'.
0.5.5a, Windows 7
I can't reproduce the problem (0.5.5b, Windows 7 x64).
After changing the partials and/or download dir (checked with directory named "test-1.2.3") all new files are saved in the right directory.
Can you add a step-by-step description how I can reproduce the problem?