I'm not seeing needle holes so this most definitely looks like an encoder issue and the pic you show appears that it is happening in close to the same spot of your design. I am thinking your encoder wheels are not making complete contact to the rails in that area and I am thinking it is the machine carriage rails that are on the "Y" axis.
These are the steps I would take:
First make sure your rack is perfectly level. Get a big carpenter's level and check every where. Both side to side and front to back with the level.
If the rails are metal clean them well with a soft cloth saturated with rubbing alcohol. Also clean the rubber on the encoders. check those rubbers well. If they are starting to dry rot or crack you may need to replace them. I'm not familiar with cruise control but my encoders have rubber "o" rings that act like "tread" and can be replaced.
Go over all the rails with super fine steel wool then clean them again with the rubbing alcohol cloth. Finally get a big piece of wax paper, wad it up in a ball and wax your rails by going over them with the wadded up wax paper.
Check where the encoder wheels connect to the arm that is holding them to make sure you don't have a little piece of thread wrapped around the axle.
Stand at the back of the machine when it is not running and slowly guide your machine to the place with the missed stitches. Stop it there and check those encoder wheels to make sure they are making good and firm contact on the rails paying special attention to the encoder that rides on the carriage rails that go front to back (the Y axis). Try to spin those encoder wheels while holding the machine stationary. if they move freely they are not making good contact.
On some encoder wheels you may have to put a weight on them so they make good continuous contact. some people adhere fishing weights to them to help or add washers.
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