Noel, the same thing has happened to me and it isn't a matter of the EQs being applied but not painting. They go flat and stay that way.
I think Sharke is saying that the project will not reset the eqs and re-loading repeatedly will alter the case and they will eventually populate. This is not the case for me. The time it happened to me recently, it was a permanent change and re-loading the project made no diff.
I'm aiming to turn on the thing that saves a version of the project every x minutes and then, if it happens, I'll send in the set of project files. I can't explain what makes it happen.
For me, the most recent time it happened to me (and maybe the only time... not sure I can remember when it happened before that), I had been bouncing with external fx and crashing a lot. Then, after a while I looked up and all my EQs were set to flat (it was only a 4 track project). But I had meticulously set the EQs and didn't know when they went flat.