Sorry for the delay in answering, I had to format my computer.
So far I could see that this problem happens on EPUB 2.0 with at least one class and attributes set for <p>.
Try like this:
1--> Create an 2.0 EPUB
2--> Copy these lines on the page's code:
<p class="noind">Non onono nono nonono,</p>
<p>nono nono nonono no no nono nonono no no no...</p>
3--> Create a CSS with these classes (of course, don't forget to link it to the page):
p{ text-indent:1.5em; }
.noind { text-indent:0em; }
4--> Save it before anything (just if you want to experiment other ways)
5--> Now, go to BOOK VIEW, join these two lines (from step 2) on the page (with backspace or del) and hit SHIFT+ENTER to separate them again but with </br> this time.
It'll look like this:
<p class="noind">Non onono nono nonono,<br/></p>
<div style="text-indent: 0px;"><span style="text-indent: 1.5em;">nono nono nonono no no nono nonono no no no...</span></div>
<p></p>