This is absolutely frustrating...though, I would certainly make a paper trail about this subject as of now before doing anything at all, regardless of what happens, it's clear like other have mentioned, the company, or atleast the CEO is willing to steal from their own employees, and is probably willing to screw you over too, if it best befits them.
No-more talking about this on the phone or anything else for that matter with the CEO on the phone, only emails. You should only answer in direct, clear questions and answers, so nothing can be ambiguously understood, you should probably attempt to figure out, if the CEO is actually stealing from their employees, or if this is just a weird thing from how their payments work, or etc before getting to angry about it however. But from what you describe, it sounds far more like theft.
If that can't be done, because the CEO knows they're doing something what seems to be illegal at worst, or shitty and shady at best, and want to avoid a paper trail and you're forced to talk on the phone, I would write down the times and dates of any calls with the CEO from now on in a notebook you keep with you and bulleted notes of the subject of each call, length, etc. Though, ideally again, you'd simply say, "I'm sorry, I can't talk about this subject over the phone, please write an email...or something around those lines"
Though, they may get clever and come in personally. At this point, it's the same as the phone call...cover yourself with documentation before doing anything else...you should also understand your contract very explicitly, to ensure that something can't backfire and be blamed on you, or some NDA things (though you said no NDA, just make sure your contract doesn't have fishy things in it anyways)
Afterwards, were it me...I'd mention it to someone who has power or influence within the company about the numbers not matching up in some prototype you started to make...it seems strange that only the commissions are short for all of the sellers...maybe they could look into something for you?
This will either start an internal firestorm when people start to notice missing money...or it'll start to show there is more internal corruption and other people know about it too.
Again, you're going to want your papertrail for the inevitability that the CEO, or someone will start stressing you about this whole subject, which might end up getting you fired. At this point, you have your paper trail to show the proper person(s) to deal with that. (suing the company for wrongful termination, going to authorities, showing the sellers, etc)
Alternatively, you could also consider whistle blowing anonymously to the local papers this may be the safest bet...though, if you're the only person who knows about this subject, beyond the CEO, well...they will know you did it...But, I guess you might not care about that anyways... :)
Again were it me, I'd do whatever I could do ruin the CEO and anyone involved once it was clear they were doing something illegal, how far you should or would go, only you can decide...a company stealing from their employees cannot be tolerated.