Hi Brian,
Per the software matrix IE9 is supported with your configuration. You can also use IE10 per the article CS151515. Am not sure which version of IE you are using.
A couple things to check.
1. Any specific action which results in this behaviour workspace getting de-activated. Also, when you say de-activated. does the connection to server still remains.
2. Are you experiencing similar issue if you change your Creo embedded browser to Firefox.
Regards
~Syed