Hi there, and welcome to our forums!
About the Misc tab:
These options are only accessible, when other settings are set properly, or a certain type of input file is loaded. When setting "Input file type" to AVI, the third option is activated. I somehow assume that the second option only is activated when a MS DV file is loaded, and/or the Canopus codec is installed.
About CCE crashing:
This can be due to various problems. At first, you can have a software problem (if you have an AMD system, did you tick the "Add resampleaudio" in the Frameserver tab?), a problem with the input file (corrupted, or wrong AVI container) or maybe even a hardware problem, as CCE really stressed your CPU and memory.
To make sure it's not a hardware problem, you can use Prime95 (use the Torture tests) to see if your system is capable of stressing.
Good luck and report back if you found out anything