Cleaning up my post. Will change this post over time as I reread through the Monster Hunter Tri thread.
NOTE: The experience of getting these to work with loaders other than CFG is not my own. These are taken from other users and how they said theirs worked. How you edit your system is complete up to your discretion and i take no responsibility for you screwing up in some way, shape, or form.
My experience:
(This is with Wanin249 rev 19 running CFG) What you're going to need is the Hermes 222/223 cios set, specifically 223 with 37+38 merging. The CSG has the complete "How-to" for installing Hermes, just, when it tells you to install 223 with x+x merged (cannot remember off the top of my head) use 37+38 as your setting. Game now works perfectly.
Nysid:
"with neogamma, u need cios 249 Rev 19 with ios37 as base ios" -From the MHT thread.
Reinstall Wanin249 rev 19 using ios 37 as the base. According to this post, this will fix your troubles.