I would try removing all of the formatting from it, also make sure it doesn't overlap into any other layout parts (IE header/footer/body), as this can cause strange behavior.
Also, it's fast becoming best-practice to build new layouts specifically for WD use. Was this layout converted from < FM11 previously?
Aside from that, I have not seen any random disappearances of objects from my WD layouts, but I've built all of my WD layouts from scratch to be purpose-oriented.
This is a new layout build from scratch, as you said. When you say to remove all formating from the button, does it mean that I can place an image, etc. in it? The button is placed inside a portal row, does it gives any problem?
I'd imagine it could certainly cause an issue. Not only are you using an image as a button, but you're also placing it in a portal! Make sure there's plenty of space around the button inside the portal row, it should not overlap the row boundary at all.
Is your button an image itself? Is it a container? Or do you have an object with an image set as a background? The latter might be a better use for buttons.
Most of the buttons I use in FMP and FMG are created the same way, using and image as a background, scaled to fit the size of the button. I would double check the space around the buttons. As I said, when they do not show up, I have to go to layout mode and modify something in the layout (i.e. adding a shape) and then it is shown again when accessing from WD. It is a refresh issue? Does it give any clue?
You said it clicks and performs the script action regardless of if the image loaded, so I think it's a loading issue.
I would be curious to inspect the "ghost" button with firebug or chrome inspector to see if the object style states it has an image set as a background. You might be able to track it down to a loading vs. a styling issue.