It's exactly what's supposed to happen - you were supposed to boot into official firmware, which should disable all possible plugins. If the buttons are still switched then either you used some form of a registery hack to re-assign buttons
or there's some form of hardware damage/misconnection involved.
To enter CFW, and by proxy also the Recovery Menu and VSH on a non cIPL-compatible PSP running 6.60, you have to use Fast Recovery which is a part of the Pro-C package for your firmware. Here's a link to the
6.60 PRO-C2 installation package, it has everything you need to enter those menus.
Technically all Fast Recovery tools should work the same, but if the one from this package does not, simply install PRO-C2 over your Custom Firmware, it features some improvements over the older C package. If you'll have any problems with the installation process, feel free to post.