As I understand it, whether or not to check "UseMMCSS" depends on your audio interface. The documentation for my Antelope Orion 32+ suggests turning it off in the DAW as it is being handled by the Antelope driver. I had better performance after turning it off in CbB.
However I don't think that is the OP issue.
Crackling audio is usually is caused by too small of a buffer. Many people have reported being able to use smaller buffers with Reaper. I have auditioned Reaper and while I like the program well enough, I did not find it to perform any better than CbB. However Cakewalk works very well on my system, so YMMV.
As far as this goes...
You should probably start a new thread. Deleting those two .ini files is not something you should have to do repeatedly. More info will be needed.