In the HTML version of the documentation generated by LATEX2HTML there are no numeric references (for example in a reference like: see section 5). Instead, the reference is displayed as a small icon. Although not obvious, this problem is closely related with the previous one. The reason why this can happen is the fact that LATEX2HTML doesn't understand the .aux file generated by pdfLATEX. So in order to get the reference numbers right execute LATEX before you run LATEX2HTML.
Notice however that references to pages will always be displayed as icons, because in the HTML version of the document, line numbers simply don't exist. If you want to solve this problem, you have to use the conditional statements of LATEX2HTML. See section 4.5 in the LATEX2HTML manual [La2HT].