Did you check around the caps themselves for a leak? Not knowing what kind you are using of course. I had issues with 2L bottles and thus changed to Ocean Spray. Much, much better seals.
Anyway, if you have broken the seal on the bottle to correct anything, it can take a bit of time to regen. Are any bubbles coming out of the seperator bottle?
Another good way to check if things are moving along is if you have clear(ish) tubing and have a small amount of water (drop or two) in the tubing. The pressure will move the water drop along the way.
* EDIT * DUH...Didn't see the mention of the Heinz bottle until I re-read it. Curious to how good of a seal you will get with those.