It looks like you are using the XSLT files on the AMCOM website. I did a compare between the "40051E_5_0.dtd" and "production-v5_0.dtd" that I use and found no code differences. I do not have alignment issues with step/sub-step numbering in my PDF output. What I use to produce my PDF output is ArborText Editor 7 with Print Composer. When I publish to PDF, I use the "production-v5_0.dtd" and "xslfo-main-v5_0.xsl" files provided by LOGSA and the default "standard.pdfcf" file by Arbortext. I do not use the FOSI files provided by LOGSA.
Be happy to look at code if you think it will help.
David