We rarely had EW, but there were 2 periods (each lasted about a week) I can remember: right around 3 months, and then again about a month ago. Owen would wake crying, just like you are describing. I'm guessing, since your LO is a BW baby, that a 'normal' wake-up doesn't involve crying. Is that true? The crying tells us they don't REALLY want to wake-up, just something is bothering: pain, poo, or sleep issues.
What happened when we had those EW - both times - is I ignored the crying! I know we're not supposed to cry it out, but I finally figured out he wasn't TRULY awake. He would seem like it - standing in his crib, eyes open - but I think he was having almost a nightmare. When I ignored the crying, ti actually stopped fairly quickly - <2 minutes - and then he went back to sleep! I was so thrilled! By the 3rd morning, he just stopped the crying altogether. I think my going in and responding at first was reinforcing whatever weird sleep habit was going on. The 5 am wakings at 3 months old also were accompanied by an early morning poo. I changed when I gave him his last feed, and that fixed those as well.
My only other thought is that he's a touch OT by bedtime if his nap is only 1.5 hours, and he's got 5.5 hours before bed. My LO pretty much can only go about 4.5-5 right now. 5.5 definitely puts us into night waking territory. I've noticed that early wakers tend not to have night wakings, and vice versa. So, it could be just a matter of bringing bedtime forward a bit. When Owen's teething, he's extra tired so I have to make sure to offer nap and bedtime a little earlier than normal.
The only other thing I notice is that his napping is different during the week and on weekends. Perhaps the inconsistency is buggering his nighttime sleep. While we were going thru the 2-1 nap transition, Owen had lots of night wakings and other night sleep problems. I think it was b/c from day to day we could never predict how much daytimesleep he'd get, or whether it would happen in 1 or 2 naps. You could try limiting those weekend sleeps a little to be closer to the weekday ones (say, no more than 2 hours) and see if that also helps.