Without seeing the whole plugin, it's difficult to say exactly where to look. You say that you're following the instructions in DITA For Print 1.8 (thank you, by the way) but you seem to be using the 2.0 version of the DITA OT. This could be one issue. There are significant differences between the 1.8 version of the org.dita.pdf2 plugin and the 2.x version, so be careful there.
Both the 1.8.5 and 2.5.4 versions of the PDF plugin transform booktitle alt into an fo:block by default (in front-matter.xsl):
<xsl:template match="*[contains(@class, ' bookmap/booktitlealt ')]" priority="2">
It looks like you changed that fo:block to fo:inline, perhaps to keep it inline with the main title? If so, you'll need to go about it another way. You can change this template to fo:inline, but then you'll need to apply that template within the mainbooktitle fo:block (assuming that's what you're doing) so that the booktitlealt becomes part of the mainbooktitle block.
For troubleshooting, when you just don't have a clue, there is always the sledgehammer method, where you comment out everything you think *could* be the problem and uncomment each thing one by one until the problem reoccurs. Be careful doing this because sometimes you can't comment out just one thing because other things depend on it, so you might have to comment out a group of things together. But in your case, I would bet the problem is in front-matter.xsl.