You best bet with with workflow is to always start by opening the file in whatever version it was created in, and then saving it out as IDML.
Do this each year before beginning the revision, to clear out trash and minor corruption in the file.
It seems counter to what you would want to do isn't IDML designed so you can convert newer files into something that older versions can open? That being said I tried it just now and in the new file created in InDesign 2015 I am getting the same results as I previously stated.
isn't IDML designed so you can convert newer files into something that older versions can open?
Yes, that is the main use of IDML, but it is also useful for cleaning up old accumulated trash and minor corruption from files. On any year-to-year project, I always run the files through IDML from the previous version before starting.
As far as your file problem, can you share the file via dropbox (or another file-sharing site)? If I could look at the file, I might be able to get a better idea what is going on with it.
CS3 files are particularly prone to sudden catastrophic damage when opened directly in CC versions. The further the version gap, the more likely you are to have trouble. If possible, you should actually export the original CS3 file to .inx from CS3, then open that in your new version, strip it down to the essentials, and save as a template. If you cannot do that, I would rebuild from scratch and save a template. Recycling files as you have been doing is a recipe for disaster down the road.