Ashley, update on this issue. After some examination we figured that both issues you encountered were bugs. Firstly, you needn't delete the folder RUT-Agent each time, the program should do it for you automatically. Secondly, the Internet ID settings that also include the address of your custom server don't apply as they should. These settings are stored in the registry, that's why just deleting the RUT-Agent folder didn't help.
We will fix these bugs in beta 3 and the final release. Meanwhile, in order to absolutely "reset" your PC's "Agent contamination status" to zero, please do the following:
1. Delete the above mentioned RUT-Agent folder in %APP DATA% Roaming before you run a new Agent.