New application that might be giving employees headaches

A team leader came to me and told me that lately some of his team members have been complaining about frequent headaches.

He made a list of things that changed during the last few months, and a major change for their team was the introduction of our new application.

He's wondering if the application might cause the headaches, or contribute to it.

I'm no medical expert, nor a safety advisor. I care about UX, but more in the sense of "this is how you create an efficient, fun to use, easy to intuitively understand application", not in a sense of ergonomics or headache prevention. Well, not yet.

I'm trying to think about what could (co)cause headaches, and what we could possibly do or try to help.

For now, I've come up with:

• Let's compare the old application and new application, and see what changed. Is the screen flashing during load times? Are there a lot more white backgrounds with black letters? Is the contrast higher, is the text jumbled/fuzzy/smaller, did we pack more information on less screen estate?
• Let's see if tools that reduce contrast or lighting (f.lux like) might help.
• Maybe it's not the physical application causing the problem, but the recent change. People have to (re)learn the new ways of working, people need time to train new habits but the workload has not been reduced to give them that time. Maybe people work longer hours to compensate, or take less breaks, or are under constant stress. It might require more of an HR solution.

We could throw a lot of money on the problem and hire big consultants or experts, but I'd like to ask the community if any of you has experience with this kind of problem, and what possible solutions or avenues exist to gain more understanding.