The first time I was deployed there 2007-08, we were all issued Doxycycline for malaria prevention. The only significant side effects that I noticed was increased sensitivity to the sun, sometimes a mild upset stomach, and the slight annoyance of having to remember to take it every day. OK, not a big deal, unless you spend almost all of your day outside in a hot, cloudless environment. Rats... Even though the uniform does a good job of protecting against sunburn and, whenever possible, I wore the sun hat (a.k.a. "boonie" hat) vice the patrol cap or helmet, I did get some sun burn. Even today, I can look at my hands and see where my sleeves stopped on my hands.
We were told that mefloquine was an available alternative and that the advantages included only having to take it once per week and it didn't increase sensitivity to sunlight. So, after about 8 months in theater, I asked to switch. A few months later, when I was getting to the end of my deployment, I noticed that I was having auditory hallucinations. I'm not talking about "hearing voices," but rather it was like I was hearing sounds differently. I would hear normal sounds to my peripheral and there would be an added intensity to it that would get my attention. It is not an easy thing to describe and I know that I'm not doing it very well. At times, I would find myself on edge. Not the "draw my weapon and turn toward the threat"-type of reaction, but rather an always on edge, always guarded reaction. Considering that we were immersed with the Aghan soldiers (speaking a different language with a different culture and considerably less educated) almost daily, it was already a stressful situation. We also knew that there were informants to the Taliban amongst the Afghan Army junior enlisted ranks. Adding a pharmaceutical factor to the mix only made it slightly more intense.
What really scared the crap out of me about it was that the change had been so slow and subtle that it had crept up on me over a period of time without me noticing it.
I immediately switched back to Doxycycline and within a couple of months the side effects were gone.
The second time I was there (2010-2011), none of the medical professionals even mentioned mefloquine as an option. I took my Doxycycline and that was it.
I am not saying whether or not mefloquine was a factor in Bales actions. I am not a medical professional. I would say, based on my experience, that if he was taking mefloquine for an extended period of time, it could have been a factor.