It's a major trust issue. You expect that when people come into your home to provide a service, they will do that particular service without violating any boundaries. Unfortunately, even with licensed companies, that is not always the case.
Regardless if this is intentional stealing or some mental health issue at work, it is a complete violation of your personal boundaries. It is really creepy to think that someone is going through your drawers and personal items. Doesn't matter why the person is doing it, it's creepy and wrong!
Also, the person may be testing you. He/she may think this is such a small thing and would seem strange to report, that you'll either not care or be too embarassed to mention it. If you let it go, however, and don't say anything, what items might be next? With behavior like this, how can you be assured that small things that you might not notice until much later or things like your personal information aren't being compromised----e.g. going through your personal papers to get CC numbers, SS numbers, bank account numbers, etc.
Regardless of the reason, this behavior has to stop. I would definitely call the service---if you were the business owner, wouldn't you want to know if something were going on with your employees rather than having all of your clients drop you and not know why?
You don't sound like a "raving lunatic" at all. After happening twice, this must be very unsettling to you. Call the owner, and simply report your observations as you've reported them here. No business owner wants to risk losing their reputation and customers. If you decide to stay with this service, you should ask for different cleaning personnel.
For everyone having service people come in, it should be standard practice to have high value items/irreplaceable items (jewelry) and paperwork with personal information in a locked drawer or file cabinet. It might seem like a pain to have to do, but it is a lot easier than having to file police reports and repairing your credit once your identity has been stolen.
Best luck in resolving this!
J. F.