I believe state law only addresses situations where the employer DID pay for your notary commission and supplies, so in the situation you describe, I'd think it's up to you. Perhaps a better question than whether or not you CAN charge your employer is SHOULD you - and that answer, IMO, would depend on a variety of conditions, starting with your attorney's attitude about it.
If you're talking about just a random signature here and there for him/her personally, then the good will you might earn from doing it for free may be worth more than the $15/sig. On the other hand, they may be more than willing to pay you because the convenience of not having to even leave the office is worth much more than that to them.
If you're talking about occasionally providing notary services for clients, then I believe you should have a discussion with your boss about that, and come to some kind of understanding in advance. Keep in mind that they ARE paying you for your time. However, as you said, you're the one providing notary supplies, etc. out of your own pocket.
This probably isn't of much help, but it's all I got...  BTW, I always wonder why people come here for questions about what's legal to do or not vs. going to the source, i.e. the Notary Handbook the SOS provides. I keep that bookmarked: http://www.sos.ca.gov/notary/handbook/. [The actual site starts with httpS, but if we take out the 's', we can create an active link here.] I don't mean to pick on you, just curious - because it happens often. 
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