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It changes the position because the position is based on the popover's dimansions and select2 changes that.
The proper way would be to style select2 (check their documentation) and then change the positionning.
If you want a quick fix for positionning you can give the popover the dimansins it used to have:
jsfiddle
I only added the dimensions for the popover to the css:
.popover{width: 249px; height: 304px;}