You really ought to supply some more hardware details, but maybe I can read between the lines. Seems you have an Atom based box of some sort and apparently have a monitor directly attached (or else you use the term console different ways in the same context). The simple answer is, don't use the serial image.
If the monitor is a temporary attachment to be replaced by an actual serial connection, then a few things. It's not usual for boot sequences to start using all available outputs but eventually the serial image is going to switch to just the serial connection. If your really are using a serial console and it's cutting out, then the most likely thing is the APU2 and pfSense have different serial speeds set and you'd have to reset you serial connection speed after it hits that point in the boot. You'll need to look up what those are, but my vague recollection from setting up my APU2 a while ago is that they are not the same or I could be thinking of the net5501. You can then change one or the other setting so they match and avoid that problem in the future.