This isn't a problem with the plug-in, just a limitation in using it on Windows servers that I thought I'd add here.
There's a 250 character limit on the total file path on Windows systems. If your cache folder is already deep (e.g., c:/inetpub/sharedhosting/domainname_com/web/blog/wp-content/cache/supercache/www.domainname.com/blog/), and you use long permalinks (i.e. post titles), then WP Super Cache will fail to cache pages if they exceed the 250 limit.
This can happen also if the temporary cache file name that PHP writes exceeds the limit (even if the final file name would not).
The only option is to reduce the root path of the cache folder, or to avoid creating permalinks that are too long.
If anyone has any ideas on how to get around this issue, I'd love to know.