It has been quite a while since I had to figure this out, so I could be misremembering, but I think you have to add your portlet to the dotlrn package paramters that list them. For example:
<parameter datatype="string" min_n_values="1" max_n_values="1" name="default_user_portal_applets" default="dotlrn_dotlrn,dotlrn_calendar,dotlrn_
forums,dotlrn_faq,dotlrn_fs,dotlrn_news" description="a csv list of the applets to call when creating the user portal template"/>
This is from dotlrn/dotlrn.info, but of course on an already installed site you would use the site map to edit the parameter. There are several of them that list applets and I'm not sure which one(s) you need to update. Doing all of them is probably safe.
