Unfortunately gedit is riddled with bugs none of which are ever addressed. The one that annoys me the most is the 'unsaved document' error where it launches an empty document as well as the document you want opened (and then asks you if you want to save it when you close down
). I know for a fact that this error has been around for at least 7 years (because I have read bug reports from 2005) but has never been addressed. I guess your error might be something similar.
There is really only one option and that is to use an editor that isn't so buggy. Pluma (although based on gedit) is miles better, but sadly pulls in shed loads of Mate dependencies when you try to install it - and that is probably not what you want (certainly not what I want). I personally go for leafpad, it is functional, lightweight and not full of bugs (at least none that affect me). There are lots of others to choose from.
If you choose this route you will obviously have to tell Thunar that Leafpad is your default text editor not gedit. I am not sure how you do that, I don't use Thunar.
OTOH it could be a bug in Thunar. I wouldn't know, as I say I don't use it.
Fujitsu Lifebook AH532. Intel i5 processor, 6Gb ram, Intel HD3000 graphics, Intel Audio/wifi. Realtek RTL8111/8168B Ethernet.Lubuntu 13.10,Ubuntu12.10 (Unity), Mint16 (Cinnamon), Manjaro (Xfce).