I don't quite understand your problem, but from what I understood the updater switched your system configuration from 2 to 1 while installing cwm.
Just change the active system to 2 in cwm and retry.
EDIT: AHHH now I understand your problem!
I'm sorry to tell you but the updater wiped out your system 1...
You see, the updater app works in 4 steps...
1. it wipes the inactive system (in your case system 1)
2. it copies the active system into the inactive one (system 2 into system 1)
3. it applies the script from the update.zip file (installs cwm in your case)
4. it switches the bootflag to boot the previously inactive system
What you experience as system 1 booting system 2 is actually the simple fact that, by using the updater app, you cloned system 2 into system 1.
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