This could actually be an issue with the way your computer is handling your IRQ channels with respect to the 1394 bus and its assignment to the IRQ channel it is on.
On Windows Vista and Windows 7 your BIOS automatically assigns your hardware to random IRQ channels and in many cases on PC's we see the 1394 bus with multiple devices on one IRQ channel. Looking at your NFO file can give you insight into how the 1394 bus is being handled and determine if there are devices that can be disabled to ensure a better connection.
To access your NFO file, Click Start > All Programs > Accessories > System Tools > System Information.
After opening the NFO file select Hardware Resources and open the Conflicts/Sharing section. You should see a Resource and a Device column. You may need to expand the columns to see the listing for your devices that are assigned to IRQ channels.
The Firewire chip will list as a 1394 Controller. If you find that your Firewire card is sharing an IRQ with multiple devices, this could very well be the issue with your drop outs of your audio. Keep in mind, this is akin to trying to send a huge steam of data through a pinched of line, sort of like when you pinch of a hose that is siphoning water, the water flow will stop as the flow has been pinched off and the amount of streaming is not sufficiant enough to keep the flow going. The same thing will happen with Audio streaming over an IRQ that is sharing multiple devices on the same bus.
In some cases, things like USB ports or High Definition Audio Controllers can be disabled to help with the 'flow' of your audio. Most things that can be disabled would be in either your BIOS or your Device Manager, if you are unsure about whether turning a device off is a good or a bad idea, you may want to contact your motherboard or computer manufacturers support and/or contact PreSonus Tech Support as well.
Typically on a Desktop computer, you could try a different PCIe card slot if your Firewire card is an expansion card and is falling into a conflict with other devices on a certain IRQ channel. You may get a more favorable result in changing the PCIe slot or adding a different card into the PCIe slot on your machine.
If you have a Laptop computer that has an Express Port slot you can purchase a Firewire to Express port adapter.
Contact Tech Support for a list of compatible hardware, typically Texas Instrument chip sets give the best results, with 2 port 400 firewire ports, combo cards are not supported.
In some cases you may find that a certain PC is a poor choice for a firewire audio interface.
Here is a tool that will test the Firewire card you have on your system: OHCI
