"et them know that you feel you're not being adequately compensated, and you've been thinking of starting a job hunt, but that your sense of loyalty dictates that you let them know now"
I absolutely would not do this. Wait until you have other offers, if you play your cards now they could withhold giving you a reference or not as good of one as you truly deserve since they know it will be to their detriment.
Do what is best for yourself, not some startup which has clearly illustrated, by the facts presented, that it does not value you as an employee. Someone else will, go find them--you owe it to yourself.
As jfarmer said above: the kind of company that takes advantage of you when you're ignorant isn't the kind of company you want to work for even after you're fully-informed and can renegotiate a better deal.