Do you have competing title tags, headings, and content between this sub-page and the home page? If they are the same or similar, something on the home page makes it more appealing to rank than your home page. It could be better quality content that is more relevant to the keyword than the home page or it could signify issues with your home page as Philip alluded to.

Limited content or mixed content on the home page could be an issue or it may be technical. Is the home page not loading correctly or loading very slowly? Also, is your home page not ranking for they keyword or is the sub-page just higher in ranking? Does your home page rank for other keywords?

It depends on what you're using the site for. If you're wondering about straight SEO results for .net or .com, there likely won't be a difference as they're both main TLDs. If the site is used for mainly one time visitors or is strictly online, you should be fine with a .net. If people are mainly getting to your site by searching or possibly bookmarking your site, it won't matter between the two.

On the other hand if you have an offline business, I would definitely go with a .com. 9 times out of 10 if you give someone a business card with MyCoolDomain.net, they will type in MyCoolDomain.com. It's just habit. Try it with friends and tell them to go to YourSite.net while standing over their shoulder. I bet even then you get most people going to YourSite.com. If it's off-line, you want people to remember the main domain and not have to worry whether the TLD is .com or .net. They just automatically guess as .com.