UserAgent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/50.0.2661.102 Safari/537.36

Steps to reproduce the problem:
1. Open http://www.bicomsystems.com/company/contact_us/
2. Select a phone number on that page (i.e. 1-954-278-8470)
3. Right click and select "gloCOM Call". It will open "glocom://1-954-278-8470", and if you have desktop application gloCOM installed, it would handle it further, so all works fine.
4. If we leave above webpage opened, and restart Chrome, on next startup steps 2 and 3 will stop working in the re-opened tab. In new tabs it will continue to work just fine.

Interesting thing is that it only affects custom protocols. For instance, if we use "http://" in our Extension, above scenario would work just fine. With "glocom://" it does not.

What is the expected behavior?
After restarting chrome, tabs that are re-opened should allow Extensions to open custom URLs from JavaScript.
In our Extension we use this code:
chrome.tabs.getSelected(null, function (tab) {
        chrome.tabs.update(tab.id, { url: url });
    });

What went wrong?
chrome.tabs.update(id, url) internally in Chrome engine fails to open custom protocol in tabs that are "re-opened" on startup. In new tabs it works just fine.
All works fine with "http://" in new and re-opened tabs.

WebStore page: https://chrome.google.com/webstore/detail/glocom-call/fmeenkjnbikclpgbonadanhnipgmofhn

Did this work before? N/A 

Chrome version: 50.0.2661.102  Channel: stable
OS Version: OS X 10.10.5
Flash Version: Shockwave Flash 21.0 r0