Having the option to allow multiple copies of Toad to run should allow you to run TDP regular and TDP workbook side by side. It works fine here and has been tested. One other person is not able to do this either.
There isn't any built in way to launch workbook from TDP regular. But you can add an External Tool to do this. Workbook is basically TDP with a different layout. You start it by using a command line arg.
"C:\Program Files\Quest Software\Toad Data Point 5.0\toad.exe" --workflowmode=true
So go to Tools|External Tools|Configure. Fill it out like below.
this will get you a launch but not necessarily fix what the issue is. if you have the multiple Toad option on there should not be any issue. Can you try to launch second toad and go to task manager and see if you have two TDPs running? Also what happens when you try to launch two regular TDPS. You should be able to do this also.