On Linux (obvious issues with testing this on Windows)...
If you try to import a file with a filename that includes a \ it can't find the file (starts looking for extra directories that don't exist).
If your using the rename function and what it should be writing out is a \ then it won't it'll write a _ instead even though a Linux filesystem can handle a \.
Obviously under Windows it should be looking for extra directories when it sees a \ on a file you've told it to import... and it should be writing _ instead of \ when using rename... but lets not let the Linux users suffer for Windows limitations please!
I personally use the tagger script to replace all the / in tags to \ so that the filenames look respectable without _ being everywhere someone has used a / in the tags.
Maybe this is really two tickets - it seems like a bug that it can't read files which have valid filenames, even if we are deliberately stripping backslashes before writing filenames.