Edit: Sticky Reload is already available since yesterday. Just download the current version or upgrade to it and you'll have the function. Ctrl-Click does *not* disable reload, the menu shown in that case is incorrect. I will fix this in the next version. Edit2: Menu bug fixed in version 1.4.2 which is already published and available for download.

Yes, reloading is disabled on purpose when you navigate away. The idea is that most (ofc not every) users only want specific pages to reload periodically, and so there should be no need to disable reloading when the page is left. There is now a new version with a new option "Sticky Reload", which will make settings "stick" across pages.