You;ve been with nobody but your boyfriend for 18 months, and you both had the all clear before and during your relationship.
You got the all clear just before you got pregnant, and after- what about 10 weeks pregnant right? So, 20 weeks, later, you get a positive.
Sometime in the last 3-4 months, you contracted it from somewhere.
The only place you could have gotten it is your boyfriend. I'm sorry to say it, but it's the only thing that makes sense.
It wouldn't take 18 months to test positive. When they say something is lying dormant in your system, it means you test positive for it, but have no symptoms-it's there, but it's dormant. If all the information you've found says it will take a maximum of 3 months to show up, that means that's the longest time it's been recorded as taking- do you know what I mean?
So you almost certainly had to have picked it up in the last 4 months, unless the first round of tests just missed it- but either way, you definately got it since you've been with your boyfriend.
Speak to him.
He needs to be tested again now too, if he hasn't been already.