If you have MFA enabled, TimeXtender will not prompt you for user+pass but only for your MFA key on subsequent opening of the application. I guess the user+pass is coupled to the Windows user signed in, which is useful in most situations.
If you have a machine with, for instance, local accounts (User1, User2, etc.) that are logged into by different TimeXtender Portal users they will not be able to pass the MFA challenge (someone else's key) and not be able to log out completely.
Apart from the fact that this is very annoying, it should be possible to set an option to force a complete login and be possible to do a complete logout. Currently you only have MFA authentication the first time and single-factor in subsequent times at worst (depending on how people secure their on-time-pass device).
This may be a hiccup that SSPs and partners can run into a bit more often than end-customers, but still something that should be smoothed out.