I can't be of much help here but I am trying to implement these mods as well, and read through this long thread about them:
http://forums.slimdevices.com/showthread.php?t=89359From what I gather, and this may not be totally right, but what I thought was a simple "change these few values" seems to be much more.
I don't really understand the programming going on at all, but from what I can tell the IRQs (is that the correct term?) can change (from log-in to log-in? upon Touch SW update? I don't know) so that some of the hard-coded "new" values actually don't get used.
So some have written up instructions to detect the actual IRQs used each time the Touch is started, and then set those values to the desired ones. I really don't know if it is necessary to get all fancy and complicated like this or not

So you may be right - A new version of firmware might have changed the IRQs and now your values don't apply to the right lines any more.
Sorry I can't help, but I'm more in the same boat trying to understand how to implement this correctly.
My system isn't set up right now so I can't evaluate any SQ changes.
-Mike