We had this problem with our LO a couple of months ago and I put it down to separation anxiety. I tried PU/PD with no success, in fact it made her worse. Then I would sit in the room with her not making eye contact but just sitting trying not to make a sound to reassure her she wasn't alone but to make clear that it was DEFO bedtime. I'm sorry to say that the problem just got worse and worse and she began waking lots during the night which she hasn't done since 10wks old (now 15 months)! SHe'd settle with me there and seemed totally sparko but the second I so much as thought about leaving she'd be back to histerics.
In the end, despite being very wary of it, I let her cry it out as the whole situation was out of control... we were all exhausted, I was very sure there was no teething or illness to blame. I think it started out as mild separation anxiety and then she thought, 'hey, it's quite good having Mum in here all the time so I'll cry'. But the good news in all of this is that she only had to cry it out three times (15mins, 5mins, 1min ish) and the problem was solved! So whilst I have never advocated crying it out as a solution, I think she got to an age of being able to figure out that her crying equalled me in the room and she started manipulating the situation.
Now to contradict myself (!) only last thought is that maybe your LO is ready for one nap and the two is taking the edge off sleep enough at night to stop him being tired enough. My LO is still transitioning and I've noticed that too much daytime sleep now equals problems at bedtime. Not sure if it helps but if she sleeps later than 3.15pm or for longer than 2hr15 in total through the day (based on 7/7.30am wake-up and 7pm bedtime) then it scuppers bed time. Even though during the morning she sometimes struggles without the nap... I've tried putting her down in her cot for 20mins quiet time in the morning at about 9.15am and that seems to be just enough to get her through till bedtime at 12.30.
Enough waffling... really hope that helps and good luck, I really feel for you.
xxx