1. Which version of cndoom and cnlauncher are you trying? Right click Properties on cndoom.exe and under Details File version should be 2.0.3.0, cnalunch.exe should be 1.4.3.0.
2. What's the full path to cndoom.exe, cnalunch.exe, IWAD and PWAD files? Are they all in the same directory or somewhere else?
3. Your OS (win98, xp, 7, 8, 7 64bit, 8 64bit, ubuntu, macox v,...)?
I really don't know why it's at the bottom of your screen, do you have two monitors? When I start in windowed mode it's centered.
Try:
1. Remove all cfg files and run setup to create new ones?
2. If you are running win7 or higher, try to right click cnlaunch.exe and run as Admin
You noticed Schyte, well, I have to see if I'll allow records for it as I really don't want to mess with COMPET-N anymore (no time), but since everything is automated now, it could be done. I have to think more about it and discuss with some people for pros and cons.
Nope, CNDOOM will not accept PWADS. It will be IWAD's only. Database is still far from perfect, I'm occupied with other stuff so it's a bit buggy right now

Sorting by columns is missing for instance and movie rows are displayed twice. There might be more but as mentioned no time. I was working on new CNDOOM lately.