I frequently see an issue with Glycerine only half registering me as being logged in identical to the issue you had above. It only happens when I first start CoH from the updater and log in my first character. Makes no difference how long I leave the game running (and there have been five- to eight- hour marathons in there).
There is, however, an easy way to work around this. At some point in the process of firing the game up from the updater, logging in, selecting your server, selecting your character, and finishing zoning in, cycle the "Force Offline" option on Glycerine. I have yet to get the half-login scenario after cycling offline and back.
Any time I see the half-login issue, Glycerine is always able to correctly identify when I quit to login and switch characters. On a character switch, Glycerine always establishes a proper connection.
(It may be worth noting that I have Glycerine in my Startup folder and I never shut it down. And since I don't routinely shut my computer down, it's quite possible for one instance of Glycerine to run for weeks without being restarted.)