Don't worry about the second one, lots of people do that when they're starting out. It's just better to have one so the rankings don't get as full, and "top 100" actually means "top 100" etc...
Yeah, that sounds like you're dealing with skipped turns problems. RoboRunner should give you similar results to the main RoboRumble (at least, in pair-on-pair scores). If you minimise the graphical interface do the results look similar to what you're getting with RoboRunner? Also, make sure you aren't running too many simultaneous threads in RoboRunner, if you're running more threads than cores it can impact skipped turns pretty heavily.
Why don't you make a page for EvBot where you explain what your general strategy is, we might be able to help you with getting it to run faster and avoiding the skipped turn problems.