When I add comments in Acrobat, after I press enter the comment only displays at 50% opacity

You can do it by running this code from the JS Console (or a button field):

this.syncAnnotScan();
var annots = this.getAnnots();
if (annots!=null) {
	for (var i in annots) {
		if (annots[i].type=="FreeText")	annots[i].opacity=1;
	}
}

After running it, right-click one of the comments, go to Properties and tick the "Make Properties Default" box, and any new comments you add after that will have no transparency, either.