I use Optiontown frequently. Mostly for AirAsia flights. Optiontown says that if you check in, it may stop you from getting the UTO upgrade, and/or the ESO extra seats, options. However I hate checking in at the last moment. Especially if they have pre-assigned me with a reasonable seat for free. I would like to know of anyone who has been UTO/ESO upgraded AFTER they have done their online check in.
I use to check-in all the time as I missed their warning not to check-in. I still managed to get a few upgrades occasionally. Whether it affects your chances we'll never know