I've made this comment before:
There is significant difference in the quality and choices. High Quality profiles are better in quality but take more time to finish. I would suggest you use the Normal or Fast profiles, they are good quality recordings and pretty fast too.
what profile are you using?
As a last option you use the old profiles and migrate them to the latest version, if you post the profile here I can help you translate it to he newer versions.
One thing is for sure, apples to apples (same profile) - the newer versions are 30% faster than the older versions of MCEBuddy - again the key is to keep the profile the same.
Old MCEBuddy did not do very well with HD video, which is primarily for hte 2 pass conversions. for SD video I would stick with Fast or Normal. Post your profile or convert to it the newer versions and see the speed difference.
Finally keep in mind, the older version was not as reslient and supported as many formats the newer version. Hope this answers all your questions.