A very similar thing has happened to me. I got my retainers just over a month ago, and whenever I take them out in the morning, it's like my bite is slightly off, and throughout the day, my teeth shift a little bit, so that my bite is normal, but then, when I put the retainers back in at night, my teeth don't fit exactly into them and they have to shift back over night. Then the whole cycle starts again the next day. It's not a huge amount of shifting, but I can definitely notice that my bite is always slightly off in the morning.
The reason I haven't contacted my orthodontist yet is because, if I have to get a new retainer, I'll have to get moulds taken again, which I never used to have a problem with, but last time I got one, the tray they were using didn't quite get all of my teeth, but they didn't have a medium sized tray, so I had to have a GIANT tray of the mould stuff in my mouth and I felt like I couldn't breathe and ended up trying to scrape it out of my mouth when it wasn't dry yet. I don't want to sound dramatic, but was one if the most traumatic experiences of my life... so yeah, unfortunately I don't have any advice for you, but I want you to know that you're seemingly in the same boat as me.