I tried to transport a project for checkup (note 1) to another computer and used the archive project button in the KiCAD main window.
On the other end I unpacked the zip and loaded the project, no problem.
But then I checked the folder and then the zip file and it’s missing a lot of stuff:
- zip files in the project folder
- .bak files
- .kicad_pcb-bak files
- subfolders are missing .xls and protel extension gerber files
What does go into the archive:
- .drl and .gbr did get packed though in the subfolders
- normal KiCAD files are going in (.sch, .net, .pro, .txt, .kicad_pcb, .lib, …)
This is on BZR6608 on Windows 7 64bit.
Will test latest nightly in due course, but it’s not my point of interest at the moment, so I postpone that after I solved my initial problem with my fab house and post a bug on the tracker if this is also in the recent version.
note 1)
Have some problems with my fab house on that kicad version it seems and wanted to compare gerber outputs with the older version of KiCAD I used that worked to see if I can find any differences in the output.
Why is it always me? 
Are the pcb fabs fully ok with rounded pads?
I am just getting my first done
no idea… didn’t switch to latest version for this project (wanted to wait till it’s out the door with the upgrade).
So can’t answer that one, but I wouldn’t expect any problems.
Did you check with a couple of gerber viewers, besides the one that is built into KiCAD?
The only thing one needs to be careful with the Chinese fabs seem to be circles (and maybe arcs?) in silkscreen etc… sometimes they don’t come (probably depending on what outdated version of CAM software they run).
I now have a different problem. Might be because I used auxiliary axis for plotting… they can see the drill file, but not the others. Didn’t change anything else… besides KiCAD version.
Fun times.
Moving design origin is something that needs careful checking, so much
could go wrong. I checked my Gerber files with Geda
Hilarious… now when I try to compare the B.Cu gerber files from each KiCAD version with the notepad++ compare plugin that one goes haywire and renders Windows unusable… graphics glitch of sorts that causes the loss of any button or text field in the windows GUI - stuff goes black or shows random parts of graphics memory I think… never had this before but can repeat it 100% with those 2 files.
Doesn’t happen with the F.Silk gerber though… 
Compared them just over the thumb by linking the vertical scrolling after that and can’t see a difference there.
So I disable the auxiliary axis option and re-submit the files, can’t do much more on my end it seems.
I hope that solves that problem for them and me. 
Hm… come to think of it.
They could read one file (note)… I submitted a paste layer gerber file stand alone as I need some small sheet metal parts made out of the stuff they use for solder paste mask.
I’m 100% certain I didn’t do the auxiliary axis thing on that one.
note:
They got back to me and asked if I really wanted that kind of paste mask cut into the metal sheet… and showed me a screenshot of it and I needed to confirm. 
EDIT.
Yes, that must be it. Checked the project… no aux axis option ticked in the plot settings for that one.
So there is hope.