Thanks for your help, that's interesting to hear. I did actually find a way to preflight for indexed colour spaces, by searching the page data for a colour profile that is listed as indexed, in case this is a problem anyone else ever wants to check a file for.
Our issue is very specific in that we do not have access to the files before they are exported as PDFs, so my main concern is checking PDFs for anything that could cause problems, so I can warn my customers and they can look into it further if they need to.
The problems we are experiencing are these: http://indesignsecrets.com/eliminating-ydb-yucky-discolored-box-syndrome.php
We have noticed that the objects that seem to produce this effect always seem to have an indexed colour space, which is presumably somehow not affected by our printers' RIP when the rest of the file is affected by it. We are powerless to change the RIP or the way the files are set up, so we just want to find a way to work out what causes this and spot it when it comes in!