Just tried to queue for both on the fleet and I was able to.
So I assume you're complaining that when one queue pops/you enter a WZ you're no longer queued for the other.
That imo makes sense.
I understand that you feel that it makes sense, but let me show this to you a logical way.
Why would a PvPer want to bother queuing for The Foundry? Because (Pre 1.4) it's easy. We know it can take a good long while for the Flash Point queue to pop, so while we wait, we run War Zones. Running War Zones passes that time for us, since we can't stand to run planet missions. Planet missions have lost their appeal, since I have ran planet missions on 6 other level 50's. I would run about 4 or 5 Flash Points a day doing this.
Wow, 1.4 is here and I can no longer stay in queue for the Flash Point when I enter a PvP match. Ouch. So at first, I queue for a Flash Point and I sit and wait...and wait...and wait...and wait...until 2 and a half hours pass. By this point I am frustrated and annoyed to a point that I log out of the game.
Well, now it's today. Now, that lesson was learned yesterday. Guess what? I don't queue for Flash Points anymore...at all. And guess what else? Neither do a few other people I have spoken to about this. Guess what else? If you are a PvP server, and you like to run Flash Points to level your character...that's a whole bunch of people who do not queue anymore, so not only does it hinder my leveling progression, but now it affects yours too.
Something people do not seem to understand about MMO...what affects me, will have either a positive or a negative affect on you, since we are all ripples in the same pond. Now, since I no longer queue anymore, it will take even longer (By an unknown percentage) for the Flash Point to queue for you. Add (Who knows how many, but I already know I am not the only person who has decided to stop queuing for Flash Points) a few dozen more players who took this same stance, and that adds to the time factor of your wait time to join another Flash Point queue.
Now take in to affect, that the timers are growing for the Flash Point queue waits and people who become less patient and aggravated over the wait times. They too begin to find the Group Finder a waste of time, and they too stop queuing. This in turn adds another pebble to the pond and causes the wait times for the Group Finder to be even longer.
The more this vicious cycle happens, the longer the queue times will be, until.....nobody queues for them at all.
So what happens now? Well, since nobody queues for the Group Finder anymore, that will force the remaining players who still wish to run Flash Points to start spamming in General Chat for teams. Which in turn is going to annoy others, so you will have flaming happening while you are trying to do so. Well well, guess what? We are right back to square one from the days before the Group Finder was created.
Simple foresight and logic.