I have noticed several times that when a piece of loot is given out the box may or may not pop up to ask what the piece of gear cost. Typically if the box doesn't pop up the gear is never recorded and goes unrecorded when I upload my snapshot. I use epgp on our website and use the epgp addon ingame to get my gear cost. Am I doing something wrong?

The popup will only come up if the item shows in the chat log.

That said, you can trigger a manual item recording by typing

/grss item

You'll want to do that whenever you've got an item that didn't prompt for cost.