Diesel Air Bubbles: Troubleshooting & Solutions

Hello,

I filled my Volkswagen Golf IV with a biofuel (biodiesel) and didn't drive it much during the first week.

After about a week, I broke down on the highway; I thought it was because the diesel filter was clogged!

As I was standing there on the shoulder of the road, removing the 'old' filter, I noticed that it was almost empty. With the new filter installed, the engine also had a hard time starting. Despite replacing the seal, there were still large air bubbles in the KS line connecting the filter to the VEP (vacuum energy pump).

After I had filled the tank completely at the gas station, everything seemed to be fine.
(This time, the correct diesel.)

Over time, I noticed that 'air getting in' always occurs when the fuel gauge is at the first mark below half full.

What could it be? Has anyone else experienced the same problems with their TDI as I have?