Are you mistakenly saving to an older version of Illustrator?
If you set up multiple Artboard in CS4, then save the file as a CS3 file, the additional artboards will be removed because CS3 doesn't support multiple artboards.
When you open old files, they retain their version number when saving.
Ah-ha! That didn't even cross my mind. That particular document had to be saved down for a different vendor than I usually work for, so that must be the issue. Thanks for the help!
I had the same issue with a CC document yesterday. Artboards are gone ... they were saved to an SVG document and there they are back again.
yorh.ekin, I am having the same issue with CC, can you help?