Converting a gradient from a spot color to a process build, hides vector elements

I have been using Illustrator for many years and consider myself very familiar with it, but recently ran into a strange issue I have never seen before.
The background element is a radial gradient with points of 0% to 50% of a spot color. The file came to me as one single layer, with the gradient in question above a vector rectangle. The rectangle shows up fine, however, until I convert the gradient from a spot to a process build at which point the box is no longer visible. The initial issue I found was that the box is beneath the gradient, but my question is why would it be visible as long as the gradient uses a spot and then disappear behind it when converted to a process build?

Version is CS5.
Part of what made the issue so confusing is that there are no effects applied. Applying the overprint feature or multiply effect don't effect the outcome either. It's only something that can be fixed by moving the gradient to a layer behind the element which is disappearing. My question is less about how to fix it (I've done that and moved on) and more about why this would happen - it seems to be a strange anomoly.
In response to the replies involving the method of color conversion:
I have used all of the methods mentioned and the end result is the same. It is starting to look to me like this is a fluke that happened with this particular file and that it is not something that can be duplicated intentionally.

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