With chrome as the default browser, when I click on a link in Thuderbird, it opens chrome, but always starts a new browser and just goes to the startup page and not to the page on the link. I am using Ubuntu 16.04. Chrome is 55.0.2883.87. Thunderbird is 45.7.0.
Go into the "Attachments" tab in "Peferences" menu and search for "http" and "https", and then change values to the browser you want or to "Allways ask". Problem solved.
If that doesn't work, you can try going to "Tools", "Options", "Advanced", "General", "Config editor". Search for "network.protocol-handler.warn-external.http" and "network.protocol-handler.warn-external.https", change both values from "false" to "true" en then try to open a link in a message. It should ask to select what browser you want to use with an option to "Remember the choice".
After all the changes I made, e.g. set Chrome as the default application in the Config Editor, Chrome would not open when I would click on a link. When I changed to Explorer it would work, but not for Chrome.
If it works in one web browser, why doesn't it work in another? I thought that, maybe during an update, the symbolic link for Chrome was changed and Thunderbird tried to open it, but with a wrong link.
So, I created a new Chrome shortcut on my Desktop and made sure that when I clicked on the icon, Chrome would open and work as expected. Then, I replaced the default application in Thunderbird with the Chrome link on my Desktop. I tried it and the link in my e-mail in Thunderbird opened in Chrome, as it always did before.
In short, create a Chrome shortcut on your Desktop, go to the Attachments tab → Preferences and change the link to the Chrome shortcut on your Desktop and click Always use this setting.