Well, once you hit FEL, you are bypassing ETT-L, so both photos aren't E-TTL so the photos don't tell the story. FEL meters the focus point which is like 3% of the frame vs. ETT-L which is metering the entire frame more or less. You're can get pretty different results between E-TTL and FEL unless the subject is very low contrast.
What it looks like to me is that since the frame is made up of high contrast with little in between, E-TTL weighted more towards the blanket leaving the baby, the subject, under-exposed. Once you hit FEL, it meter the baby, which I assume is the focus point, so now the baby is properly exposed and the blanket is a bit over-exposed.
E-TTL is no different that any other auto setting on the camera; it doesn't know what your subject is, it's just going to try to make everything look as uniform as possible.
That said, that can explain these two photos, but have you experienced this under-exposure in different conditions? Because the most logical explanation for these two is that the E-TTL just missed.
At worst, the 580 II can bracket flash, so you can experiment and find out where you need to dial the compensation with that lens.
Canon Rebel XSi | Canon EF 17-55mm | Canon EF 50mm 1.8 | Tamron 70-300mm VC USD | Canon 430