I'll just note that, in Chrome, when I first start my browser and X-Notifier (v3 or v4) first checks for new mail... it only checks my primary Gmail and leaves my second and third accounts unchecked (as well as my mail.com accounts). All my other accounts are checked fine.
HOWEVER... once the check interval time elapses, ALL my accounts are checked from then on (including Gmail and mail.com accounts). I don't know why, and it's not a major problem for me to waste time fussing over.