If you have configured many VDOMs on your system, past the default ten VDOMs, this could easily be your problem.

Each VDOM you create on your FortiGate unit requires system resources to function - CPU cycles, memory, and disk space. When there are too many VDOMs configured there are not enough resources for operation. This may be a lack of memory in the session table, or no CPU cycles for processing incoming IPS traffic, or even a full disk drive.

Go to System > VDOM and see the number of configured VDOMs on your system. If you are running 500 or more VDOMs, you must have a FortiGate 5000 chassis. Otherwise you need to reduce the number of VDOMs on your system to fix the problem. Even if you have the proper hardware, you may encounter noticeably slow throughput if you are using advanced features such as security profiles or deep content inspection with many configured VDOMs.