If IzoT Commission Tool (IzoT CT) isn't working properly (for example, you are missing some CT dialogs) then the Visio Trust Center settings may not be configured properly.
Open Visio 2016 directly (not through IzoT CT). Click the “File” Menu (you may need to create a Blank Drawing first before you see the Visio Menus), click “Options” and then “Trust Center” (in the Visio Options dialog) followed by click the “Trust Center Settings …” button.
Trusted Documents: Make sure the "Allow documents on a network to be trusted" is checked and "Disable Trusted Documents" is unchecked.
Add-Ins: All checkboxes should be unchecked.
ActiveX Settings: Make sure "Enable all Controls without restrictions and without prompting" is selected, and "Safe mode" is checked.
Macro Settings: Make sure "Enable all Macros" is selected and "Trus access to VBA project object model" is checked.
File Block Settings: All check boxes should be unchecked