I would like to add to @Kerosia's answer, specifically his line
It's also likely that a church's decision to run same-gender groups is based on a number of factors, only one of which is a Biblical argument.
Source: I am a youth group leader in our church and we do segregate for small group and prayer. As we only have youths, @Kerosia's bible verse doesn't about the younger women learning from the older ones doesn't apply here. We have talked about it in leadership meeting and I think our thoughts is what most churches base this practice on:
The goal of small group is to grow closer to God. It is a place where we can share our struggles with sin (besides other things) and pray for them, learn from others on how they live out God's commands and ask questions about God. Ideally, the leader sets and example of this and inspires the youth to open up themselves and participate in this kind of spiritual growth. In order to get others to participate, we have to create an atmosphere where everyone trusts the others. Doing this in gender-mixed groups creates problems to this intimacy.
Crushes. Young people, often in their teenage year, are especially susceptible to this (and good for them). This is strengthened by that fact that they know their parents want them to find someone christian, and this is in most cases the only christian network. If a person has a crush on someone in the group, he certainly is less willing to share his deep struggles, and often even his questions about God, because he doesn't want to say something that could make his crush like him less. Separating the groups according to gender removes this problem. Moreover, someone with a crush has most of his attention focused on this person, rather than paying attention to the discussion.
Gender specific topics. Whether or not you have a crush, most guys don't want to talk about their sexuality/pornography when girls are around. Likewise, girls won't open up about their periods or crushes (I don't actually know what they talk about). Later in life this topics include wife, finances & job related problems for the men, while women focus more on motherhood & relationships. An additional, but a little less important factor is similar interests like sports, cars & machines on the guys side
Missing trust. Furthermore, because of their brain structure, same-sex groups tend to think more alike and therefore to build trust more easily, not just about the gender specific topics, which is a huge factor because trust is essential for people to open up.
While problem 1 gets less important with age, problem 2 gets increasingly important, especially when married, as one often doesn't have much time to spent time with friends other than in smallgroup.
In most churches, this is not a hard rule, but it is applied when they want to facilitate trust and intimacy, for example in prayer. The basis for this is not directly biblical, but is rooted in a biblical worldview which states that the genders are different (See genesis 1) and takes into account these differences when planing the service.
As for the studies describing the effect of gender-segregation, I assume (and could be wrong) that this described the effect of complete segregation (for example girls only school). At least in our church, we encourage attendants to get to know each other all the time (we share worship, input, bible study and have time reserved for people to stay and talk after our official program). Because the gender-segregation is only the exception for the specific activities of praying and deep group discussions, I don't think described the negative effect of the studies would apply.
There is a fair argument to be made that deep group discussions don't need to be segregated because there is no trust required (at least just for the discussion), in practice however they are often related to struggle with sin (trust required) and are followed by prayer. This is why we separate deep discussions (personal) and bible study (less personal).
The reasons for gender-segregation are often not directly biblical based, but come from the psychological differences of the genders and how this affects trust in a group, which can be traced back to a biblical worldview.