From the sounds of it, it sounds like you downloaded this file while connected directly from your internet connection, rather than the VPN. The VPN itself will tunnel absolutely ALL of your internet traffic through the VPN server so that your ISP cannot see what you are doing, and by the same token, to the internet, you will appear as being somewhere other than where you really are.
As for the server error 500, I'm not sure what to say to that, as you seem to be the only person to experience this issue.
Now as for the speeds, this does make sense as most ISP's will automatically throttle your connection speed once they detect any kind of P2P traffic passing through your connection. When you're connected to the VPN on the other hand, all your ISP will see is your connection to the VPN, without being able to tell anything more.
As for having been "found out", this is likely a case of a copyright troll started IP sniffing through the peers list and found your IP address associated with an active P2P connection while you were downloading the file. This can easily be skirted around through the use of a VPN as this will mask your IP address to the internet as being that of your VPN, rather than that of your ISP.
