Well I tried in Sonar X3 and it had the same behavior as Reaper so it's now looking more like the issue lies with EKS. Funny thing is that .fxp files saved in both Reaper and Sonar will load in FL Studio but won't load in themselves. So it seems like the fxp files are not corrupt since they load in FL but there is just something in the way EKS is interacting with Reaper and Sonar when trying to re-load the patches. I normally only use EKS in FL Studio so never noticed this before.