pfSense

No,I din't configure pfsense to use /dev/cua0.What happened was that I changed WAN type to DHCP,PPP,etc and saved those configurations and then tried to set it back to PPPoE to see if it would fix it.
Unfortunately it didn't...

Indeed if you change from PPP to PPPoE you'll have /dev/cuau0 remained in <ports></ports>.

Whenever you set up WAN to PPP section <ppps><ppp><ports> in config.xml changes to whatever you shoos in "modem port" - for example /dev/cuau0. Then it is always presented in <input name="ppp_port" type="hidden" value="/dev/cuau0"> in interfaces.php. From now on you can't properly change WAN to PPTP or PPPoE as you can't get back em1 (or other ethernet interface), the page just does not provide you a choice for that.
I think "modem port" was wrongly introduced on this page interfaces.php as it links logical interface WAN-PPP to physical interface /dev/cuau0. All logical-physical links are defined under Interfaces->(assign), so this should go there as well. Or another way: physical part should be brought ino interfaces.php for PPTP and PPPoE.

Forgot to mention: now user can always fix the mess he got after several reassignments by going to Interfaces->(assign) and choosing proper interface.

Sorry to insist but the problem showed up after a change in config.I deactivated the interface and when I activated it it never worked again.The switch with the interfaces was later when I was changed WAN type to see if it would fix it.
The original change that cause the problem was NOT change of WAN type!

Then create separate Bug report describing the problem.

I created this bug describing my problem and its enough for me.
I will wait for the new release.
Thanks