Hmmm. Weird. I've been using "Regular expression" for search mode, so it isn't that.
I've decided to just copy and paste the necessary sections from the latex files and transform those into html. The Sigil search finds the paragraph indent and extra line in the latex, and I can replace with paragraph tags that way no problem. I'll need to do a few other replaces as well, but it shouldn't take too long.
Thanks for checking it out for me.