Absolutely not, if they can be addressed in a scientific manner. For example, the lack of fossils of what many refer to as "transitional species" might be considered a problem by some, but that can be addressed using our knowledge of what it takes to become a fossil. Only a miniscule proportion of anything that's ever lived will become a fossil, and we can't expect to find a fossil of every species that's ever lived.
I was really referring to the Cambrian Explosion....but now that you bring us to the lack of missing links...if one species were evolving over a period of millions of years, you'd expect to find a hybrid at least once. So, you have no physical evidence of evolution occuring in the past...instead, you have sudden appearance and statis.
I have a few problems with Behe's approach to research. First, saying something is "too complex" for us to understand is a judgement call and open to interpretation. Prior to the understanding of gravitational forces, I suppose someone looking at the orbiting of planets and moons, etc. would say that this process is "too complex" and that it simply must have been designed that way. I guess what it boils down to for me is that once you say something is "too complex" to be understood without the consideration of a designer, you've effectively closed the door on examining the phenomenon using the scientific method. Imagine how many things we as humans would have never discovered if everyone agreed that certain things were too complex to be understood without consideration of a designer. Magnetic forces, electroreception, polarized light, etc. could all be considered some of the things not easy to see and examine, thus they might have been potentially attributed to a designer; however, careful scientific investigation has given us tons of information on these cryptic aspects of our environment. Behe's research approach also exhibits the problem I highlighted earlier...mainly that he came up with a conclusion first and is looking for observations to support it (not the approach required by the scientific method).
I love how this argument is abused so much…But you miss the positive point…Behe is making an argument that naturalistic processes cannot explain irreducibly complex systems, which then (should) lead to intense study of such systems in an attempt to prove him wrong. So, far from stopping science, it should stimulate science. And what's really annoying about your argument is that many scientists who did study the very things you mention were Christians who believed God had created the world. Also, I don't see how saying certain forces were designed would stop science either. I know someone made my computer…but I am majoring in computer engineering so I can understand how these bloody things work…just admitting something is designed does not stop one's interest in understanding how. Science is about how, not why, correct? And, if I forgot to ask it once, what is wrong with starting with an assumption and building a theory from there? I mean, the idea of macroevolution is over 3,000 years old, the Greeks were the first to think of it, and Darwin, being a deist, must have believed that all life came about naturalistically. But you do not apply your rules to your own beliefs. No, you can't, because your argument cuts both ways. And I think you're playing with definitions. Behe came up with a hypothesis, then went for the evidence. He did not conclude at first that certain systems were designed, quite the contrary.
Can I hear ANY new arguments against ID...
Maybe if we mass import some Muslims which basically make it the only option to believe in Allah (God) or DIE, we could win back God. That might teach the ever increasing population of atheists to back down from their position. So this is what it will come to, huh? Don't you just love to hate the education system or what have you for pressing their "scientific human origins" belief on the uneducated to turn them to atheists? DIE INFIDELS!!! 
