Well, I had nothing better to do, so I counted EVERY SINGLE MEDAL manually, and tabulated everything into a nice excel file.
1) NG does not account for 2245 of my points. I do not know why this is so. This is too large a number for me to guess which medals/games are not being calculated properly. I can only guess that the games under the new "beta" medal system mentioned before are the ones screwing up, but I suppose only PsychoGoldfish knows the details.
2) The medal points/count for each game on wylo's page is pretty much accurate. I noted a few discrepancies though (perhaps due to removed/added medals, but the discrepancies are pretty small). Here is the list, with the corrected total medal points/count:
1. Time Fcuk 270/9
2. Blasting Agent 170/6
3. Pico's Ludo Vengeance 405/9
4. Greek & Wicked 140/4
5. Touch the Bubbles 3 530/12
6. LARRY: Gnomergeddon 535/11
7. Quick Sand 130/4
3) NGLOGS DOES EVERYTHING CORRECTLY, as far as I can tell, down to counting 0 point medals. Thus, if in any doubt, refer to it.
If anyone is interested in having the excel file for your own use, let me know.