Boilovers suck, dont they ? 😉
First question, did you top up your wort after the boilover to maintain the 10L final batch ? that would be the most obvious reason for a low OG - dilution. 1.039 vs 1.044 isnt much of a difference tbh - I doubt you'll be able to tell in the finished brew.
To know whether your efficiency is lower will require repeat batches - if you're still consistantly low after 3-4 batches, then adding in a few 100g's of extra grain will cover it.