You might experience, that the Area field might be handled differently in FogBugz projects, and some of your new cases are not having set as default the Undecided Area.
FogBugz has an Autosort engine aimed at helping sorting incoming emails easier and quicker, also it is filtering out spam messages. Based on your previous updates to incoming emails it learns which emails to which Project and Area should be assigned.
If you would like to disable this autosort functionality, you can do it by changing the Sorting configuration of the Mailbox to Manual Sorting and configuring the default Area to Undecided.
The sorting can be configured separately for each Mailbox you use.