I think some people may be in the same boat I was. I'm going to explain environment I was in, the symptoms I experienced, and what I did to get back to 'normal'.
1) I was on Bionix Fusion 1.1 with the Core kernel. I have a non-voodoo compatible nand chip (nothing noteworthy there, but thought I'd share if any commonality appears). I had EXT2 lagfix set.
2) Reboot to clockworkmod recovery, install rom from sd card, browsed to Macnut R2 and flashed.
3) Never unplugged usb cable. Rebooted, froyo comes up and I begin to play. I completely foobar'd my backup because I sync Titanium to dropbox, and believed I'd actually sync the other way, but ended up deleting all my backups. Oh well, so I feverishly installed apps for a good 30min.
4) I was able to adb push at this point. I pushed my titanium license file over and the launcher2.apk in the OP.
5) Noticed the media scanning was stuck at 0%. I remembered seeing things about this in the thread, so I did a bit of a search. Got terrified by what I saw.
6) Unplugged phone, went home, plugged in there... ADB shell works.
7) Brought up clockwork rom manager, and tried to reboot to recovery. It times out, sometimes (not every) it would display an error (sorry, don't have it exact): Sorry! Recovery process is not running. Something to that effect.
8) Tried ADB reboot recovery. Times out.
9) Nerveously reboot phone to see if the problem 'goes away' a la microsoft
10) Reboots into same state. Media Scanning. However, now I can't ADB. I get "Device Offline".
11) Freak out.
12) I was able to get into clockwork mod recovery by rebooting and holding the vol up/vol down. I don't know why this was so easy to get into, and I may be lucky as some have hardware locks... but this worked for me. Sigh of relief for me.
13) First step I took was to push another kernel and flash that, see if it resolves the issue. Flashed, rebooted. Usb cable in the whole time.
14) No change.
15) Went back into recovery the hardware way. Pushed macnut r2 to the sdcard again. Flashed once. Realized I should clear dalvik cache and battery stats, so did that and then flashed a second time (third overall if you count the first flash).
16) For no reason other than trying different things, I then unplugged the usb and rebooted. This was the first time I rebooted after the flash w/o the usb plugged in.
17) I let it boot the first time and didn't touch it until media scanning completed.
Ta-da, success. This is not a science, but it is all the steps that I went through, and perhaps it can help another person out there. I had heavily contemplated flashing back to another 2.1 rom/kernel when I successfully got into recovery, but thought it was worth a shot to just try once more. It luckily did work for me.