Here's how I do it:
When converting to MOBI, make sure you have "debug" turned on. After the conversion, go to the "processed" folder in wherever you put the debug output. Edit the content.opf in there and add this line to the <guide> section:
<reference href="mybook.html#start" type="start" title="Startup Page"/>
(Obviously, substitute your HTML file and anchor in there.)
Then, zip all the content in that processed folder and add the zip to Calibre. Convert that zip to a MOBI and it will retain your start page.