Hello Tania.
I think you may be using .scmignore wrongfully. Are you using Workbench, Eclipse Plugin or command line (hrefresh/hsync)?
On the Workbench/Eclipse Plugin, you can use Ignored Resources facility (set once for the whole project) and the .scmignore file (that has to be present in each directory you want to customize/filter).
On the command line (hci, hrefresh, hsync, etc) you can only provide a list or pattern to include files, not to exclude them.
Does this help?
Best regards,
Ricardo Bernardino