This problem started earlier this year after a PortableApps update. I didn't track which one, I just ignored it and worked around it thinking it would be fixed in the next update. Nope.
When having PortableApps start Firefox and Thunderbird automatically, and then clicking on a link from Thunderbird, PortableApps tries to open another Firefox and then gives the dreaded "Another instance of Firefox is already running" error box. The only times this occurs are when both are set to start automatically. If only one or the other is set to start automatically, and then the other is started manually, everything works. If only Thunderbird is set to autostart, then clinking on a link starts the other and works. if neither are set to start, and are started manually, it works. I even registered FirefoxPortable.exe with windows as the browser to use as posted a few other places but it had no effect.
The ONLY time I have the problem is when both are set to start automatically on startup of portable apps.
I have been unable to cause the problem with any other method of using the apps.
Is this some timing problem caused by overlapped starting automatically?
It always starts Firefox first, do you think telling it to start Thunderbird first would work, and if so, how do I do that?