Years have passed since the OP started this thread and I am using Windows 10 Pro 64bit, so the root cause might be different, but I am sharing my experience, maybe it will help someone else too.
I realized, that in my case, the Focus assist feature in Windows was preventing the Evernote note window to pop to the foreground. I had to turn off all options (see highlighted with the red rectangle), which resolved my issue. First I tried to add Evernote to the priority list and change the settings to priority only, but I couldn't figure out how as Evernote was not offered as an option in the apps list, so I have decided to turn the feature off completely. I will revisit it if notifications get too annoying. :)