After seeing tens of threads involving issues with flashing using ROM manager, and no warning thread, I decided to post this.
If you're rooting for the first time, or upgrading recovery Do Not Use ROM Manager. It simply does not work properly for the Tf101. This may change in the future if the dev adds official support, but for now, please avoid like the plague.
Install recovery with this instead: http://forum.xda-developers.com/show...very+installer
Gnufabio did a good job making a working recovery installer.
After you flash this, if you want to upgrade your CWM go to the development forum and flash the new CWM .zip using the version installed by recovery installer. Hope this saves some people some trouble, Thanks!