LOL...yep, astute of you to notice.
Well, that's good but somewhat bewieldering...you've got me stumped for the moment...
I actually have the program source for jcase's 1-click app (he kindly sent it to me). There is nothing special or different about what his app is doing versus what my Gscript script does outside of the fact that I tweaked and recompiled a different version of Amon_RA's custom recovery source to build the one you've been trying to flash.
I also see that you replied about ClockworkMod recovery...that's good news and you are exactly right about it doing "funny" (bad) things to some phones.
Since you seemingly can "recover" (re-install) your recovery by re-running jcase's 1-click app, you could try running the "1.6.2" version and see if it behaves any differently (if you read my thread, you'll see the stuff about how I arrived at building the two different versions).
If you are proficient and/or gung-ho, you could also try "Scenario 4" and manually flash the custom recovery via the Android SDK using the adb.exe utility to invoke flash_image from the command line.
If you do know how to install and use the Android SDK and the adb utility, you actually can use these tools to wipe and flash ROMs without needing to use touch the phone (i.e., if your trackball isn't working). This is done by connecting to the phone while booted into Amon_RA custom recovery and interacting with the adb server that is up and running while custom recovery is running. From there, you can issue (relatively cryptic) commands to wipe and flash a ROM.
You can't use fastboot since you don't have the S-OFF bootloader (i.e., step E in Scenario 4).
I know that eu1 has previously subscribed to this thread, but I don't know if he's out there watching at the moment, but I really would like to get his take on what might be happening here...
I'm not sure what else to tell you at this point unless you want to pursue the SDK / adb route...
Thanks, and sorry for the long responses....