Hello
I will need more information,
what Windows server are you using?, have you tryied unisntall the installer and reinstall it agian? (only the installer)
which version of the installer are you using? (if you click the ? mark in the dashboard will show the about window showing the version of the installer)
which version of the workbench are you trying to use?
are you able to make a clean install?
I have a new environment, isnatlled 5.6.25 server 64 bits with workbench 32 bits, in Windows 8.1 64 bits, and another with Windows server 2012 and I wasn't be able to see any error like you said, perhaps a step by step could help us to try to reproduce your error.
respond the questions and also try to uninstall the installer and install again, if is an older versión tan 1.4.8 please download the latest bundle from our site.
or fill a new bug in
http://bugs.mysql.com/ adding step by step the process to reproduce this error