404 errors on permalinks related to Classifieds content

We have been trying for months to resolve an issue with the classifieds which we have implemented with some custom fields and in our case called "Listings". We initially assumed that the problem was related to another plug-in but after disabling just about every plug-in only the Classifieds plugin remains.

When we save the permalinks custom as http://innovationdistricts.org/%postname%/ it works for a few minutes and then reverts back to returning 404 errors on Classified related content only.

Especially these links stop working
which you can find on
http://innovationdistricts.org/exchange/ shown as red, blue, yellow image links displayed as "View Existing..."

My client is of course beoynd upset. Your assistance will be greatly appreciated.