merge in RapidSVN has different results than with command line

I've been using svn in a linux environment from the command line for a while and some of my windows using co-workers want to get on source control bandwagon. We've chosen to use RapidSVN because the client exists for Mac, 'nix and Windows.

I'm running into a problem with merging.
When I merge from the command line, additons, deletions and modifications all end up in my target copy.  However, not so with RapidSVN.

Firstly, in the log message window, it only shows updates, when I know that there should be additions (new directory with files).
Secondly, none of the files are actually modfied, either on the filesystem or in the RapidSVN right hand pane.

I suspect that it might be user error, because the information you pass to RapidSVN for a merge is a little different than you do with svn from the command line.

This is what I've been doing.
1) updating both the working copy of the branch and trunk
2) entering the path for the working copy branch in the first working copy box, with the latest revision as shown in the Log
3) entering the path for the working copy trunk in the second workign copy, with the lastest revision as shown in the log
4) entering the path for the working copy trunk in the destination path
5) keeping recursive checked

When I click OK, the log message reports

Execute: Merge
Updated: /tmp/trunk/control/xxxxx.ctl
Updated: /tmp/trunk/control
Updated: /tmp/trunk/bad
Updated: /tmp/trunk/bin/xxxx.lst
Updated: /tmp/trunk/bin/xxx.ksh
Updated: /tmp/trunk/bin
Updated: /tmp/trunk
Updating...
Ready

But none of the additions (new directory and files show up).  Then if I check the status with the command line, these files don't show up as modified...

Is this user error on my part or is the "merge" in RapidSVN supposed to perform differently than a svn merge command?

Thanks for your help.

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