Yes, you need to flash the boot image if you are S-ON...
But save the headaches and don't even bother flashing a ROM from your installed recovery (you really don't even need to install a custom recovery at all), all you need is the "recovery.img" from the recovery ZIP file of choice, although I currently recommend TWRP, in your adb directory and the ROM on your SD card then...
1) Reboot into Hboot and start Fastboot, connect PC
2) Type "fastboot boot recovery.img" and wait a minute for the Recovery to start on the phone
3) Wipe as per normal for installing a ROM
4) Install/Flash ROM zip as per normal
5) Reboot and enjoy!
Current Personal Phone: Google Nexus 4 (KitKat 4.4.1 KOT49E/AT&T GoPhone SIM)
Current Work Phone: HTC Rezound on VZW (S-OFF/CarbonROM
Current Tablet: iPad 4 and Nextbook 8 Premium with marxo's N8+ ROM - Revision 1b2 (ICS 4.0.4)
Previous/Retired Android Devices: HTC Aria, HTC Incredible 2, Samsung Stratosphere, HTC Rezound, Samsung Galaxy S2 Skyrocket