2009 Vw Eos Owners Manual
I havent ever had this problem but i'm familiar with the eos so i can say almost undoubtedly that the you have a bad trunk latch. There is a switch in the trunk latch that tells it if it's closed or open and i'm guessing that the switch is bad.
2008 Vw Eos Owners Manual Pdf
Once the switch tells the car that the trunk is closed, it runs the motor that close the trunk fully. However, i say again that i've never had this problem on an eos so there is a fair amount of room for other issues. Volkswagens are rather complicate and use a lot of different switches and such in the convertible top. Also, the only way to know for sure is to bring your vehicle to the vw dealer becuase only the vw 5051 scan tool is capable of reading the inputs and outputs of the convertible top control module and this is what is required to properly diagnose the problem.
2008 Vw Eos Owners Manual
Don't waste your time throwing parts at it, the dealer should be able to give you a 100% positive diagnosis with one hours labor (about $90) Mar 28, 2010.