Similar problem here.
I'm running pfSense 1.2.1 live from the CD as a test, in hopes that it can be used more permanently.
I've got an alias defined that contains the same ports (80,443,3389), and in the same order.  80 is the first port defined in the alias.
I have a NAT rule using this port alias that has automatically created a firewall rule for me,
and… this rule works for me over port 80, but not over port 443.
If however, I add an additional NAT rule that specifies port 443 instead of referencing my port alias, and give that rule higher precedence over that of the rule using the port alias,
my test is a success... even across port 443.
I too would like to know if I have overlooked something.
Any suggestions you can offer are more than welcome.
Thanks