Custom Rom problems

[froggerhopper]

Has anyone else had problems trying to install roms like cyanogenmod after the Jellybean update? I used to be able to install CM9 nightlys then eventually stable releases and back to stock with no problems, so i am not a noob to flashing roms. Now after I updated to stock 4.1 I cant install CM10 or any other custom roms. I have tried installing through CWM and TWRP but cant get past the ASUS screen after flashing the usual way. In fact, I cant even install Stock JB anymore through recovery. I have to flash it through ADB. I heard there was a change in partition sizes when the update applied. Is there a way to install custom roms again or am i doing it wrong now?