You said you have seen the problem on a PC with onboard "re" LAN.
Suggestion:
Put your cards on that PC. Install or boot pfSense. At interface configuration time specify you want to use VLANs and configure two VLANs, one for WAN and one for WAN. At the later prompt specify option 8 to get a shell prompt. Then type
dmesg | more
which will display the startup output a screenfull at a time. Use a digital camera (or phone) to capture the who startup output and post it somewhere we can look at it.
I suggest using pfSense 1.2.3-RC3 or one of the RC3 snapshot builds to get the most up to date hardware support.
Here's an example of sartup output showing an attach failure which resulted in the device not being available. (This is to give you an idea of what to look for.)
re0: <realtek 8168="" 8168b="" 8168c="" 8168cp="" 8168d="" 8111b="" 8111c="" 8111cp="" pcie="" gigabit="" ethernet="">port 0xd800-0xd8ff mem 0xf7eff000-0xf7efffff,0xf7ee0000-0xf7eeffff irq 18 at device 0.0 on pci4
re0: Chip rev. 0x3c000000
re0: MAC rev. 0x00400000
re0: PHY write failed
re0: PHY write failed
re0: MII without any phy!
device_attach: re0 attach returned 6</realtek>
I believe in this case the problem was fixed in a later version of pfSense.