If the contents of both panes change "behind" Tux Commander, either because both directories change or because both panes display the same directory, then you need to refresh both panes individually.
IMHO this is non-intuitive, Ctrl+R should always refresh both panes, even if this can have a performance penalty in some cases.
... sorry, forgot to mention: I'm using version 0.6.50-dev from Debian sid (unstable).
Regards,
Andrei