Please try toggling the "View/Show Transparent Windows" button. Just be aware that it may also cause the mouse cursor to flash or blink on the remote machine. It may also cause a slight slow down in performance as well. Some applications (and tool tips) use some type of non-standard method(s) of drawing items on the screen, and the Windows API calls that the Mini Remote control (DMRC) program uses are unaware that these items exist. Therefore, they are displayed on the physical desktop of the remote machine, but not in the MRC window.
However, you can also use the new DameWare Mirror Driver as well to connect. It's included in all 5.x & 6.x versions of the software.
For version 5.x of the software, you first have to connect to the remote machine and install the Client Agent Service, just as always. Next, provided the remote machine was running Windows 2000 or greater, you could select File / Mirror Driver Installation and then follow the prompts (may or may not require a reboot of the remote machine).
For version 6.x, you simply have to install version 6.x of the MRC CLient Agent Service on the remote machine, and the Mirror Driver will automatically be installed the first time you connect to this machine with version 6.x of the software.
Once it's been installed on the remote machine, you can then enable the "Use MRC Mirror Driver if available" in the Remote Connect dialog to use the Mirror Driver to retrieve video (instead of the traditional method of scraping the screen). How to install and remove the DameWare Mini Remote Control's Mirror Driver. http://www.dameware.com/support/kb/article.aspx?ID=300077
I hope this helps.