I had submitted gerbers that were generated by the latest stable version of KiCAD. They were rejected as a problem (only drill file visible) by the board house. I came to this forum and saw the problem with negative coordinates in the gerbers. I moved the design in KiCAD so that there were no negative coordinates and then resubmitted the files. The following week the gerbers were rejected by the board house with the same problem as the first time they were rejected (drill file only visible). After doing some research on other forums, I concluded that the first line in each gerber (something like "%TF.FileFunction,Copper,L2,Bot,Signal*% ") was causing a problem with their software. I removed this first line and the boards were completed and the status shows that they have been shipped.
There appears to be multiple problems with the gerbers that KiCAD generates and the particular board house's software. I have submitted KiCAD gerbers to other manufacturers without first molesting the gerbers files and had them made with no problem. It seems to be a problem with this particular board house.
Unfortunately, the KiCAD problem just bit me too. I submitted files multiple times until I looked in this forum and found the information about KiCAD. I moved the board as described and verified that there were no longer negative Y coordinates in the gerbers. Hopefully, they will go through now. I submitted them before the new ordering page came on line.