I have the same issue.
I have used Web vSphere and can get the console to work there with no issues.
I submitted ticket to VMWare... but since Thinapp Factory is not 'supported'... they were not willing to troubleshoot.
Hope someone finds an answer... Since auto-capture has rarely worked for me, I am not going to be using TAF until I have the ability to use the manual capture feature.
A slight workaround that occasionally worked was to open console from vSphere after starting the Manual Capture process. But even that didn't always work.
Until then I am capturing without TAF.