Stanza 3 Summary

Get out the microscope, because we’re going through this poem line-by-line.

It was no dream, I lay broad waking;
But all is turned thorough my gentleness
Into a strange fashion of forsaking;

The speaker insists that the whole kiss thing wasn't a dream, but real. He was wide-awake, he swears! Whatever you say, buddy.
Before we get ahead of ourselves, let's clarify some more of these rather old-fashioned phrases. The phrase "thorough my gentleness" means through my gentleness, or because of my gentleness. "Forsaking" means abandoning and "fashion" means habit or way.
So basically, even though he was totally nice to her (our guy's ever-the gentleman), this girl totally gave him the cold shoulder. No more late night visits. Harsh!
Apparently, the speaker's "gentleness" has somehow caused her to do this. Maybe he should have played hard to get. Or something.

And I have leave to go of her goodness
And she also to use newfangleness.

The speaker and his late night visitor appear to have some sort of open relationship arrangement. Because she's so good, he's allowed to go chase other women. And she, too, is allowed to pursue other guys.
"Of her goodness" means "because of her goodness," or "because she is so good." But we've seen nothing so far that makes her seem good at all, so maybe our speaker's being a little ironic – you know, saying one thing while meaning just the opposite? He is upset, after all. "Newfangleness" is an old word (Wyatt actually stole this quirky word from its first inventor – Chaucer) that means a "fondness for novelty or new things," or the act of being "easily carried away by whatever is new." To put it simply, this girl is fickle. It's not exactly a nice word, and it suggests our girl is, shall we say, less than monogamous. She'll spend time with whatever dude catches her wandering eye next.

But since that I so kindly am served,
I would fain know what she hath deserved.

This is a strange conclusion, right? Our guy is wondering what this woman deserves as a result of her kindness towards him. Or at least, that's what it sounds like at first.
Kindly can have two possible meanings, though. For one, it could mean that he has been kindly treated, as in, she treated him nicely. But our speaker sure doesn't seem thrilled with her, so perhaps he's being ironic again?
Maybe. But kindly can also mean doing something in a way typical of one's "kind." In other words, the sentence could mean "since you're treating me in a way typical of females" or "since you're treating me the way I have treated you."
And finally, "Fain" means "gladly." So our speaker would "gladly" like to know what the woman deserves for her behavior, because he sure doesn't have a clue.
This line could have a couple of different meanings. First, it could mean that he thinks this woman has behaved badly, and might deserve punishment, because women shouldn't be making such promiscuous sexual advances. Then again, it could also mean that he thinks she deserves something better than just a midnight tryst, because she's a good person.
Either way, it seems our speaker doesn't quite know how to treat this lady because none of the typical rules of relationships seem to apply to this new, "strange" situation. Before, when he had all the power, things were pretty simple. But now that she appears to be the one in charge, our boy's in the weeds.