I'm guessing it just seems harder...however, since the run leg of the race is the last leg...it may be more beneficial to have it setup this way since your body will grow accustomed to running when not fresh.

That being said:
How big of a break do you take between workouts...is it a true brick? If so, how many times are you doing this (multiple per week)?...you may be overtraining and benefit some from just doing 1 workout a day at least every so often

Sorry you had to switch things around, but just the thought of 4 a.m. runs in Houston gave me the willies!
One of the best pieces on advice I ever got was to run off the bike on a regular basis, not a brick mind you, just a short transition run of about 10 minutes to get the legs used to that kind of stuff. That being said...It's not ok to do brick workouts everyday. Some plans have them up to three days a week, others only three to five times in a cycle.A reminder here that a brick is a bike followed by a substantial run of 20 minutes or more, or a swim followed by a good spin on the bike. There can be long run bricks or long ride bricks...they take many forms. Bricks should be done once in awhile. They are hard on the body. So hard that many plans will have you keep the run at an easy (or zone 1 ) pace. An everyday brick can lead to injury and burnout. (I know from experience.) If you could do one of the workouts later in the day that would be ideal. Some will say that it's better to get in one longer well executed workout a day, in a specific discipline, than two workouts, one of which is mediocre.
From what you said, it sounds like your body is adapting and that takes time...too, maybe you are not fueling enough before or during the first workout to give the gas to make it through the second. It does you no good to make to the second workout and have your form fall apart and be unable to have a good quality workout.
Best of luck with the changes!

As jsk85 said....there are bricks and there are two a days. Depending on the time between them. Too many bricks will cause negative effects as Anton said.
Two-a-days have some recover time so you can do them more often. You'll have to see if it's getting used to the new routine or overtraining. Keep track of your resting HR. Typically this gets elevated if you are overtraining (or on allergy medicine in my case). Or occasionally just do one long workout instead. You'll figure it out.

What they said. A couple of decent brick workouts before your race is all ya need. Two-a-days or just focusing on one event is the way to go.

Shooot... I only do 1 brick a week. Saturday mornings at 530 I'll head out for a high intensity 30-40 mile bike and then a solid 9 mile run. thats usually enough to kick my butt for the day, if I have anything left I'll try to get a swim in later in the day. Sundays are a slow but long ride 80-150 with a group. During the week I only hit maybe 4hrs of real intense training but it's enough for me and I'm lookin forward to IMWI!

So.. depending on what race you're lookin at and how well you want to do. But 2 a days everyday... that's euro cool.

Well...I do a swim/bike brick every time I ride mid week (2-3 times). Since I could swim every day with no risk of injury I don't see a reason why not to add on a bike ride to it. Seems to work for me though. Bike/run bricks are another story...do those infrequently anymore.

I usually do my run/bike brick in the right order, but when i double it usually ends up in the wrong order. when i swim double i swim in the evening because i feel like the chlorine clogs my pores or something because i never feel the same after i get out of the swimming pool and try to run or bike. When i double bike/run i end up running first, then biking after dinner because i can get on the bike and hammer away with a full stomach no matter what i ate, but if i drink milk or have anything spicy i have issues on the run.

I work from 5am-2pm and my mom (luckily i am fortunate enough that she still cooks for me) likes me to be home for dinner at 5:30, so if i double this is the best i can do.