Why am I only getting email notifications of our Membership applications and not our entries?

If I understood correctly you are not getting the Email Notification from one of the forms that is shared with your account. To exactly which form is your issue related to? Please provide us the form URL.

I checked our email logs and all emails from several different forms were successfully sent to your email address. 

Please check your spam folder and if there are emails coming from @jotform mark them as not spam.