Merge audio regions does WHAT exactly??

Umm.. So, I select a bunch of audio regions that sound fine.. I hit "=" and click "create" to the non-contiguous audio regions require the creation of a new audio file...
I am presented with an audio part that is distorted... How is this happening, I don't recall this being the way things are suppose to go (once again, HA HA).
So this is the before:
and this is the after:
And it sounds distorted, so something is actually happening to my audio during the mixdown. Is this still related to my corrupted file, or am I missing a checked feature in preferences that says "ruin and distort audio when merging regions" ?
So, if I select my regions and copy them and paste them into a new song, their lengths & fade areas are all messed up.. And if I mix down, they are distorted and all messed up...
AAAA!!!!
I guess I need to turn off plugins set my 1-2 to 0db and bounce everything..
Thank you.
-patrick

if you merge stereo files on a mono track it it sums the two channels into a mono file. Set the track to stereo and the problem should go away.

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