The Media Companion media search is recursive, people have multiple methods of organisation and this ensures that media is not missed.
The problem you are encountering is probably related to rar archive files. Since media companion can playback directly from within a rar archive (incliuding multipart), MC needs to support this as a media format.
The problem, as you have stated is that other rar files, such as subtitles can be wrongly identified as media.
MC contains an option to set the size of rar files to ignore, its located in the general preferences. If you have no media in the rar format then just set this to a large size. The default I believe is set to 8Mb, which is larger than most subtitle files, any rar files smaller than this setting will be ignored.