I'm sure some of the same things that make Pence a lower middle of the lineup hitter in the past are in vogue now. Meaning he is too much of a free swinger for the upper part of the lineup, however he can provide some run producing power hitting. It speaks to being a #6 hitter for pretty his prowess as a hitter. Having said that, the other reasons he may be hitting in that spot is because of the propensity for opposing pitchers to decide to pitch around the true middle of the lineup hitters.
IOW - if Bourn and Tejada fail to get on, then a pitcher has no need to pitch to a Berkman and Lee. Berkman, for his part, will take the walk if necessary, leaving the onus to bring him or Lee in on the 5 and 6 hitters. If you don't have a quality stick at those spots, then you're going to get some pitchers who will never give anything to Lee and Berkman. Now, if Bourn and Tejada do get on, then a pitcher has to think that he still has Berkman and Lee (more disciplined hitters) to face rather than a free swinger who can possibly reward him with an out with such an approach. Makes facing Berkman and Lee easier, or less painful.
The other thing is what JA mentioned, Tejada is just hitting too well right now and doing an great job as a #2 to consider moving him and Pence (swaping one for the other). Plus, it bears repeating, Pence is his own worse enemy when he starts to swing at everything thrown at him. At his best, Pence forced the pitcher to come to him and Gunther thus made strides towards being an elite hitter. As is, if the opposing pitcher doesn't make mistakes with him and they do sometimes, Pence will have to prove once again he ain't swinging at just anything. Right now, he's a very good mistake hitter and to make an opposing pitcher prone to making mistakes is to put Pence in situations that will allow for such challenges.
